Sun May 12 22:31:08 UTC 2024 I: starting to build heudiconv/experimental/i386 on jenkins on '2024-05-12 22:31' Sun May 12 22:31:08 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_12/10946/console.log Sun May 12 22:31:08 UTC 2024 I: Downloading source for experimental/heudiconv=1.1.1-1 --2024-05-12 22:31:08-- http://cdn-fastly.deb.debian.org/debian/pool/main/h/heudiconv/heudiconv_1.1.1-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2252 (2.2K) [text/prs.lines.tag] Saving to: ‘heudiconv_1.1.1-1.dsc’ 0K .. 100% 251M=0s 2024-05-12 22:31:08 (251 MB/s) - ‘heudiconv_1.1.1-1.dsc’ saved [2252/2252] Sun May 12 22:31:08 UTC 2024 I: heudiconv_1.1.1-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: heudiconv Binary: heudiconv Architecture: all Version: 1.1.1-1 Maintainer: Debian Med Packaging Team Uploaders: Michael Hanke , Yaroslav Halchenko Homepage: https://github.com/nipy/heudiconv Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/heudiconv Vcs-Git: https://salsa.debian.org/med-team/heudiconv.git Testsuite: autopkgtest-pkg-pybuild Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3-all, python3-datalad, python3-filelock, python3-setuptools, python3-pytest, python3-nipype, dcm2niix, help2man, python3-dcmstack, python3-tinydb, python3-inotify, python3-duecredit, python3-dicom Package-List: heudiconv deb science optional arch=all Checksums-Sha1: 99ad2509d966ef784df847bd2228143496e48e22 9161019 heudiconv_1.1.1.orig.tar.gz bc86fcc6a5c111c8103b4e3857340fa1b827346b 4468 heudiconv_1.1.1-1.debian.tar.xz Checksums-Sha256: 30a642b25993190138dbea1fbfcaebfb93b46a545be8312397fad9003e57372e 9161019 heudiconv_1.1.1.orig.tar.gz 6b9c68d9c7776f79929cfc90f6d9156bf3d944445dddd186275d4e7625e3b823 4468 heudiconv_1.1.1-1.debian.tar.xz Files: ee69ac6daed90b15a380b6b5863e714a 9161019 heudiconv_1.1.1.orig.tar.gz a9967b9366041016ee2a82c36c71d763 4468 heudiconv_1.1.1-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEEj23hBDd/OxHnQXSHMfMURUShdBoFAmY9/jIRHHRjaGV0QGRl Ymlhbi5vcmcACgkQMfMURUShdBroOBAAjBqAqvVyU5UnGcDusc8Y+8C2tVIUy6dZ nfWoKgtkVHVkOCuTV9ewZPjRW/EEiHfzsEUvXDqDL9BF7kvgh0aTdNWseaboofwv HPZu0+yUkJjOuamlyZcggkOhzZBtwMKtlpstVo1Duz7R5xrmDTpL0QeORjCPW6e5 B7q8khR5NFotcB7t5VCeXdKxfVKn5pBRzvEgeS2ekPH5zYsuZuYBFoCOpCsTyFTh dGalb4ScxJejpeMHFc0Llthn7LexaqUraI33ReMcClBVvp4qXEz15VgUv7RDrFyt uSCahxPp0OUkmF2LuykTCLlfu9pTioQYeRzBpQqpQsxXswTqEI3o7by/qGAa9Wvj YHD48w/wudai/7Mh8AFL65369iCVKsO4+vDSIwVaBVNoSEeLd7QHq9fi9npFlUTO /xeohTXDIuKBpK77EpY+jrpHAFB+vcmDzPlAHsyeUkH1jvfzaGQt7hQHMdoQatkE Vlq+3M2CBszWXvOaw9lF3pLZtyVF+QgixY/s1+52tuN60Q6X07D1BBL+UdD2+/Lc c6oOIAdyWGKZtZmvW8hkyYyIhgcshPs8RVMH7LmtouCjO4J/yIbqExvLgnynHYV/ EJJi1/sXEgNHajvSp0zNx9tb6bTNGDZO36tc+t5kYGMDNvUjrIRylnNTwsZHNpnq Fry8hQH+kpw= =pfhJ -----END PGP SIGNATURE----- Sun May 12 22:31:08 UTC 2024 I: Checking whether the package is not for us Sun May 12 22:31:08 UTC 2024 I: Starting 1st build on remote node ionos12-i386.debian.net. Sun May 12 22:31:08 UTC 2024 I: Preparing to do remote build '1' on ionos12-i386.debian.net. Sun May 12 22:35:58 UTC 2024 I: Deleting $TMPDIR on ionos12-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun May 12 10:31:10 -12 2024 I: pbuilder-time-stamp: 1715553070 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/experimental-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [heudiconv_1.1.1-1.dsc] I: copying [./heudiconv_1.1.1.orig.tar.gz] I: copying [./heudiconv_1.1.1-1.debian.tar.xz] I: Extracting source gpgv: Signature made Fri May 10 11:00:02 2024 gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A gpgv: issuer "tchet@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./heudiconv_1.1.1-1.dsc: no acceptable signature found dpkg-source: info: extracting heudiconv in heudiconv-1.1.1 dpkg-source: info: unpacking heudiconv_1.1.1.orig.tar.gz dpkg-source: info: unpacking heudiconv_1.1.1-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying deb-no-demand-on-etelemetry I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/7723/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 ' DISTRIBUTION='experimental' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='4cdd68029e9a45ee81ac07b0c1d8c606' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='7723' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.NSBXfzzp/pbuilderrc_cjia --distribution experimental --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.NSBXfzzp/b1 --logfile b1/build.log heudiconv_1.1.1-1.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos12-i386 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 6 07:34 /bin -> usr/bin I: user script /srv/workspace/pbuilder/7723/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, python3-all, python3-datalad, python3-filelock, python3-setuptools, python3-pytest, python3-nipype, dcm2niix, help2man, python3-dcmstack, python3-tinydb, python3-inotify, python3-duecredit, python3-dicom dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19684 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-datalad; however: Package python3-datalad is not installed. pbuilder-satisfydepends-dummy depends on python3-filelock; however: Package python3-filelock is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-nipype; however: Package python3-nipype is not installed. pbuilder-satisfydepends-dummy depends on dcm2niix; however: Package dcm2niix is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on python3-dcmstack; however: Package python3-dcmstack is not installed. pbuilder-satisfydepends-dummy depends on python3-tinydb; however: Package python3-tinydb is not installed. pbuilder-satisfydepends-dummy depends on python3-inotify; however: Package python3-inotify is not installed. pbuilder-satisfydepends-dummy depends on python3-duecredit; however: Package python3-duecredit is not installed. pbuilder-satisfydepends-dummy depends on python3-dicom; however: Package python3-dicom is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: 7zip{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} curl{a} dcm2niix{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} git{a} git-annex{a} git-man{a} groff-base{a} help2man{a} intltool-debian{a} libaec0{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libbsd0{a} libcbor0.10{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdebhelper-perl{a} libedit2{a} libelf1t64{a} liberror-perl{a} libexpat1{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgssapi-krb5-2{a} libhdf5-103-1t64{a} libhdf5-hl-100t64{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} libldap-2.5-0{a} liblocale-gettext-perl{a} liblzf1{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libopenjp2-7{a} libpipeline1{a} libpopt0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libsub-override-perl{a} libsz2{a} libtool{a} libturbojpeg0{a} libuchardet0{a} libxml2{a} libxslt1.1{a} libyaml-0-2{a} libyaml-cpp0.8{a} lsb-release{a} m4{a} man-db{a} media-types{a} netbase{a} openssh-client{a} openssl{a} p7zip-full{a} patool{a} po-debconf{a} python3{a} python3-all{a} python3-annexremote{a} python3-appdirs{a} python3-certifi{a} python3-cffi-backend{a} python3-chardet{a} python3-charset-normalizer{a} python3-ci-info{a} python3-citeproc{a} python3-click{a} python3-colorama{a} python3-cryptography{a} python3-datalad{a} python3-dateutil{a} python3-dcmstack{a} python3-decorator{a} python3-deepdiff{a} python3-dipy{a} python3-dipy-lib{a} python3-distro{a} python3-distutils{a} python3-duecredit{a} python3-etelemetry{a} python3-fasteners{a} python3-filelock{a} python3-funcsigs{a} python3-gitlab{a} python3-h5py{a} python3-h5py-serial{a} python3-humanize{a} python3-idna{a} python3-importlib-metadata{a} python3-iniconfig{a} python3-inotify{a} python3-iso8601{a} python3-isodate{a} python3-jaraco.classes{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jeepney{a} python3-jsonpickle{a} python3-keyring{a} python3-keyrings.alt{a} python3-lib2to3{a} python3-lxml{a} python3-minimal{a} python3-monotonic{a} python3-more-itertools{a} python3-msgpack{a} python3-networkx{a} python3-nibabel{a} python3-nipype{a} python3-numpy{a} python3-ordered-set{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pkg-resources{a} python3-pluggy{a} python3-prov{a} python3-psutil{a} python3-pycryptodome{a} python3-pydicom{a} python3-pyparsing{a} python3-pytest{a} python3-rdflib{a} python3-requests{a} python3-requests-toolbelt{a} python3-scipy{a} python3-secretstorage{a} python3-setuptools{a} python3-setuptools-scm{a} python3-simplejson{a} python3-six{a} python3-tinydb{a} python3-tqdm{a} python3-traits{a} python3-trx-python{a} python3-typing-extensions{a} python3-tz{a} python3-urllib3{a} python3-zipp{a} python3.11{a} python3.11-minimal{a} python3.12{a} python3.12-minimal{a} readline-common{a} rsync{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: aria2 bind9-host git-remote-gcrypt gnupg graphviz ipython3 javascript-common krb5-locales less libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lsof mayavi2 nocache pigz publicsuffix python3-bottleneck python3-bs4 python3-clevercsv python3-cssselect python3-fuse python3-gdal python3-html5lib python3-httpretty python3-jinja2 python3-matplotlib python3-numexpr python3-odf python3-openpyxl python3-pil python3-pydot python3-pydotplus python3-pygments python3-pygraphviz python3-pyperclip python3-sklearn python3-sparqlwrapper python3-tables python3-vcr python3-vtk9 python3-xvfbwrapper python3-yaml xauth 0 packages upgraded, 183 newly installed, 0 to remove and 0 not upgraded. Need to get 156 MB of archives. After unpacking 784 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main i386 liblocale-gettext-perl i386 1.07-7 [15.1 kB] Get: 2 http://deb.debian.org/debian unstable/main i386 libpython3.11-minimal i386 3.11.9-1 [817 kB] Get: 3 http://deb.debian.org/debian unstable/main i386 libexpat1 i386 2.6.2-1 [107 kB] Get: 4 http://deb.debian.org/debian unstable/main i386 python3.11-minimal i386 3.11.9-1 [1918 kB] Get: 5 http://deb.debian.org/debian unstable/main i386 python3-minimal i386 3.11.8-1 [26.3 kB] Get: 6 http://deb.debian.org/debian unstable/main i386 media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian unstable/main i386 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian unstable/main i386 tzdata all 2024a-4 [255 kB] Get: 9 http://deb.debian.org/debian unstable/main i386 readline-common all 8.2-4 [69.3 kB] Get: 10 http://deb.debian.org/debian unstable/main i386 libreadline8t64 i386 8.2-4 [171 kB] Get: 11 http://deb.debian.org/debian unstable/main i386 libpython3.11-stdlib i386 3.11.9-1 [1795 kB] Get: 12 http://deb.debian.org/debian unstable/main i386 python3.11 i386 3.11.9-1 [602 kB] Get: 13 http://deb.debian.org/debian unstable/main i386 libpython3-stdlib i386 3.11.8-1 [9336 B] Get: 14 http://deb.debian.org/debian unstable/main i386 python3 i386 3.11.8-1 [27.4 kB] Get: 15 http://deb.debian.org/debian unstable/main i386 libpython3.12-minimal i386 3.12.3-1 [809 kB] Get: 16 http://deb.debian.org/debian unstable/main i386 python3.12-minimal i386 3.12.3-1 [2224 kB] Get: 17 http://deb.debian.org/debian unstable/main i386 libpopt0 i386 1.19+dfsg-1+b1 [45.8 kB] Get: 18 http://deb.debian.org/debian unstable/main i386 rsync i386 3.3.0-1 [428 kB] Get: 19 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.22 [22.4 kB] Get: 20 http://deb.debian.org/debian unstable/main i386 openssl i386 3.2.1-3 [1364 kB] Get: 21 http://deb.debian.org/debian unstable/main i386 ca-certificates all 20240203 [158 kB] Get: 22 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3 [314 kB] Get: 23 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3 [114 kB] Get: 24 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3 [42.9 kB] Get: 25 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.21-14+b1 [162 kB] Get: 26 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 27 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-4 [1194 kB] Get: 28 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40-8 [97.2 kB] Get: 29 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.7-2 [39.7 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 man-db i386 2.12.1-1 [1421 kB] Get: 31 http://deb.debian.org/debian unstable/main i386 libbsd0 i386 0.12.2-1 [134 kB] Get: 32 http://deb.debian.org/debian unstable/main i386 libedit2 i386 3.1-20230828-1+b1 [97.8 kB] Get: 33 http://deb.debian.org/debian unstable/main i386 libcbor0.10 i386 0.10.2-1.2 [30.8 kB] Get: 34 http://deb.debian.org/debian unstable/main i386 libfido2-1 i386 1.14.0-1+b2 [87.4 kB] Get: 35 http://deb.debian.org/debian unstable/main i386 libkrb5support0 i386 1.20.1-6+b1 [36.1 kB] Get: 36 http://deb.debian.org/debian unstable/main i386 libcom-err2 i386 1.47.1~rc2-1 [22.8 kB] Get: 37 http://deb.debian.org/debian unstable/main i386 libk5crypto3 i386 1.20.1-6+b1 [83.2 kB] Get: 38 http://deb.debian.org/debian unstable/main i386 libkeyutils1 i386 1.6.3-3 [9432 B] Get: 39 http://deb.debian.org/debian unstable/main i386 libkrb5-3 i386 1.20.1-6+b1 [360 kB] Get: 40 http://deb.debian.org/debian unstable/main i386 libgssapi-krb5-2 i386 1.20.1-6+b1 [145 kB] Get: 41 http://deb.debian.org/debian unstable/main i386 openssh-client i386 1:9.7p1-4 [991 kB] Get: 42 http://deb.debian.org/debian unstable/main i386 7zip i386 23.01+dfsg-12 [1671 kB] Get: 43 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-4 [293 kB] Get: 44 http://deb.debian.org/debian unstable/main i386 autoconf all 2.71-3 [332 kB] Get: 45 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 46 http://deb.debian.org/debian unstable/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 47 http://deb.debian.org/debian unstable/main i386 autopoint all 0.21-14 [496 kB] Get: 48 http://deb.debian.org/debian unstable/main i386 libbrotli1 i386 1.1.0-2+b3 [314 kB] Get: 49 http://deb.debian.org/debian unstable/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-6 [20.5 kB] Get: 50 http://deb.debian.org/debian unstable/main i386 libsasl2-2 i386 2.1.28+dfsg1-6 [60.6 kB] Get: 51 http://deb.debian.org/debian unstable/main i386 libldap-2.5-0 i386 2.5.17+dfsg-1 [198 kB] Get: 52 http://deb.debian.org/debian unstable/main i386 libnghttp2-14 i386 1.61.0-1+b1 [84.0 kB] Get: 53 http://deb.debian.org/debian unstable/main i386 libpsl5t64 i386 0.21.2-1.1 [57.4 kB] Get: 54 http://deb.debian.org/debian unstable/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b4 [62.0 kB] Get: 55 http://deb.debian.org/debian unstable/main i386 libssh2-1t64 i386 1.11.0-4.1+b2 [225 kB] Get: 56 http://deb.debian.org/debian unstable/main i386 libcurl4t64 i386 8.7.1-5 [478 kB] Get: 57 http://deb.debian.org/debian unstable/main i386 curl i386 8.7.1-5 [352 kB] Get: 58 http://deb.debian.org/debian unstable/main i386 libopenjp2-7 i386 2.5.0-2+b3 [197 kB] Get: 59 http://deb.debian.org/debian unstable/main i386 libturbojpeg0 i386 1:2.1.5-3 [216 kB] Get: 60 http://deb.debian.org/debian unstable/main i386 libyaml-cpp0.8 i386 0.8.0+dfsg-6+b1 [144 kB] Get: 61 http://deb.debian.org/debian unstable/main i386 dcm2niix i386 1.0.20220720-1+b1 [261 kB] Get: 62 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 63 http://deb.debian.org/debian unstable/main i386 libtool all 2.4.7-7 [517 kB] Get: 64 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB] Get: 65 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 66 http://deb.debian.org/debian unstable/main i386 libsub-override-perl all 0.10-1 [10.6 kB] Get: 67 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 68 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 69 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.191-1+b1 [194 kB] Get: 70 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 71 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-4+b1 [9549 kB] Get: 72 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.9.14+dfsg-1.3+b3 [727 kB] Get: 73 http://deb.debian.org/debian unstable/main i386 gettext i386 0.21-14+b1 [1311 kB] Get: 74 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 75 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 76 http://deb.debian.org/debian unstable/main i386 debhelper all 13.15.3 [901 kB] Get: 77 http://deb.debian.org/debian unstable/main i386 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 78 http://deb.debian.org/debian unstable/main i386 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 79 http://deb.debian.org/debian unstable/main i386 python3-distutils all 3.12.3-1 [131 kB] Get: 80 http://deb.debian.org/debian unstable/main i386 python3-setuptools all 68.1.2-2 [468 kB] Get: 81 http://deb.debian.org/debian unstable/main i386 dh-python all 6.20240422 [107 kB] Get: 82 http://deb.debian.org/debian unstable/main i386 libcurl3t64-gnutls i386 8.7.1-5 [468 kB] Get: 83 http://deb.debian.org/debian unstable/main i386 liberror-perl all 0.17029-2 [29.0 kB] Get: 84 http://deb.debian.org/debian unstable/main i386 git-man all 1:2.43.0-1 [2112 kB] Get: 85 http://deb.debian.org/debian unstable/main i386 git i386 1:2.43.0-1+b1 [8906 kB] Get: 86 http://deb.debian.org/debian unstable/main i386 libyaml-0-2 i386 0.2.5-1+b1 [55.2 kB] Get: 87 http://deb.debian.org/debian unstable/main i386 git-annex i386 10.20240129-1+b1 [22.5 MB] Get: 88 http://deb.debian.org/debian unstable/main i386 help2man i386 1.49.3 [198 kB] Get: 89 http://deb.debian.org/debian unstable/main i386 libaec0 i386 1.1.3-1 [24.5 kB] Get: 90 http://deb.debian.org/debian unstable/main i386 libblas3 i386 3.12.0-3 [140 kB] Get: 91 http://deb.debian.org/debian unstable/main i386 libgfortran5 i386 14-20240429-1 [733 kB] Get: 92 http://deb.debian.org/debian unstable/main i386 libsz2 i386 1.1.3-1 [7824 B] Get: 93 http://deb.debian.org/debian unstable/main i386 libhdf5-103-1t64 i386 1.10.10+repack-3.3 [1178 kB] Get: 94 http://deb.debian.org/debian unstable/main i386 libhdf5-hl-100t64 i386 1.10.10+repack-3.3 [74.4 kB] Get: 95 http://deb.debian.org/debian unstable/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 96 http://deb.debian.org/debian unstable/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 97 http://deb.debian.org/debian unstable/main i386 libjs-sphinxdoc all 7.2.6-7 [150 kB] Get: 98 http://deb.debian.org/debian unstable/main i386 liblapack3 i386 3.12.0-3 [2167 kB] Get: 99 http://deb.debian.org/debian unstable/main i386 liblbfgsb0 i386 3.0+dfsg.4-1+b1 [29.1 kB] Get: 100 http://deb.debian.org/debian unstable/main i386 liblzf1 i386 3.6-4+b1 [10.1 kB] Get: 101 http://deb.debian.org/debian unstable/main i386 libpython3.12-stdlib i386 3.12.3-1 [1945 kB] Get: 102 http://deb.debian.org/debian unstable/main i386 libxslt1.1 i386 1.1.35-1+b1 [243 kB] Get: 103 http://deb.debian.org/debian unstable/main i386 lsb-release all 12.0-2 [6564 B] Get: 104 http://deb.debian.org/debian unstable/main i386 p7zip-full all 16.02+transitional.1 [2560 B] Get: 105 http://deb.debian.org/debian unstable/main i386 patool all 2.0.0-2 [39.3 kB] Get: 106 http://deb.debian.org/debian unstable/main i386 python3.12 i386 3.12.3-1 [659 kB] Get: 107 http://deb.debian.org/debian unstable/main i386 python3-all i386 3.11.8-1 [1056 B] Get: 108 http://deb.debian.org/debian unstable/main i386 python3-annexremote all 1.6.4-2 [15.9 kB] Get: 109 http://deb.debian.org/debian unstable/main i386 python3-appdirs all 1.4.4-4 [12.5 kB] Get: 110 http://deb.debian.org/debian unstable/main i386 python3-certifi all 2023.11.17-1 [155 kB] Get: 111 http://deb.debian.org/debian unstable/main i386 python3-cffi-backend i386 1.16.0-2+b2 [114 kB] Get: 112 http://deb.debian.org/debian unstable/main i386 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 113 http://deb.debian.org/debian unstable/main i386 python3-charset-normalizer all 3.3.2-1 [51.6 kB] Get: 114 http://deb.debian.org/debian unstable/main i386 python3-ci-info all 0.3.0-1 [7584 B] Get: 115 http://deb.debian.org/debian unstable/main i386 python3-lxml i386 5.2.1-1 [1990 kB] Get: 116 http://deb.debian.org/debian unstable/main i386 python3-citeproc all 0.6.0-3 [96.7 kB] Get: 117 http://deb.debian.org/debian unstable/main i386 python3-colorama all 0.4.6-4 [36.2 kB] Get: 118 http://deb.debian.org/debian unstable/main i386 python3-typing-extensions all 4.10.0-1 [66.2 kB] Get: 119 http://deb.debian.org/debian unstable/main i386 python3-more-itertools all 10.2.0-1 [59.9 kB] Get: 120 http://deb.debian.org/debian unstable/main i386 python3-zipp all 1.0.0-6 [6696 B] Get: 121 http://deb.debian.org/debian unstable/main i386 python3-importlib-metadata all 4.12.0-1 [24.9 kB] Get: 122 http://deb.debian.org/debian unstable/main i386 python3-click all 8.1.7-1 [94.0 kB] Get: 123 http://deb.debian.org/debian unstable/main i386 python3-cryptography i386 42.0.5-2 [1272 kB] Get: 124 http://deb.debian.org/debian unstable/main i386 python3-distro all 1.9.0-1 [20.3 kB] Get: 125 http://deb.debian.org/debian unstable/main i386 python3-monotonic all 1.6-2 [5728 B] Get: 126 http://deb.debian.org/debian unstable/main i386 python3-fasteners all 0.18-2 [14.0 kB] Get: 127 http://deb.debian.org/debian unstable/main i386 python3-idna all 3.6-2 [37.0 kB] Get: 128 http://deb.debian.org/debian unstable/main i386 python3-six all 1.16.0-6 [16.3 kB] Get: 129 http://deb.debian.org/debian unstable/main i386 python3-urllib3 all 1.26.18-2 [116 kB] Get: 130 http://deb.debian.org/debian unstable/main i386 python3-requests all 2.31.0+dfsg-1 [68.6 kB] Get: 131 http://deb.debian.org/debian unstable/main i386 python3-requests-toolbelt all 1.0.0-2 [40.0 kB] Get: 132 http://deb.debian.org/debian unstable/main i386 python3-gitlab all 1:4.3.0-1 [72.8 kB] Get: 133 http://deb.debian.org/debian unstable/main i386 python3-humanize all 4.9.0-1 [52.0 kB] Get: 134 http://deb.debian.org/debian unstable/main i386 python3-iso8601 all 1.0.2-1 [15.7 kB] Get: 135 http://deb.debian.org/debian unstable/main i386 python3-jaraco.context all 4.3.0-1 [7616 B] Get: 136 http://deb.debian.org/debian unstable/main i386 python3-jaraco.functools all 4.0.0-1 [10.6 kB] Get: 137 http://deb.debian.org/debian unstable/main i386 python3-jeepney all 0.8.0-3 [34.0 kB] Get: 138 http://deb.debian.org/debian unstable/main i386 python3-secretstorage all 3.3.3-3 [16.1 kB] Get: 139 http://deb.debian.org/debian unstable/main i386 python3-jaraco.classes all 3.2.1-4 [7232 B] Get: 140 http://deb.debian.org/debian unstable/main i386 python3-keyring all 25.2.0-1 [53.6 kB] Get: 141 http://deb.debian.org/debian unstable/main i386 python3-pycryptodome i386 3.20.0+dfsg-1 [1086 kB] Get: 142 http://deb.debian.org/debian unstable/main i386 python3-keyrings.alt all 5.0.1-1 [17.5 kB] Get: 143 http://deb.debian.org/debian unstable/main i386 python3-msgpack i386 1.0.3-3+b1 [101 kB] Get: 144 http://deb.debian.org/debian unstable/main i386 python3-tqdm all 4.66.4-1 [90.8 kB] Get: 145 http://deb.debian.org/debian unstable/main i386 python3-packaging all 24.0-1 [45.5 kB] Get: 146 http://deb.debian.org/debian unstable/main i386 python3-datalad all 0.19.6-2 [889 kB] Get: 147 http://deb.debian.org/debian unstable/main i386 python3-dateutil all 2.9.0-2 [79.4 kB] Get: 148 http://deb.debian.org/debian unstable/main i386 python3-pydicom all 2.4.3-1 [1120 kB] Get: 149 http://deb.debian.org/debian unstable/main i386 python3-numpy i386 1:1.26.4+ds-8 [5469 kB] Get: 150 http://deb.debian.org/debian unstable/main i386 python3-decorator all 5.1.1-5 [15.1 kB] Get: 151 http://deb.debian.org/debian unstable/main i386 python3-scipy i386 1.11.4-6 [19.0 MB] Get: 152 http://deb.debian.org/debian unstable/main i386 python3-nibabel all 5.2.1-1 [2659 kB] Get: 153 http://deb.debian.org/debian unstable/main i386 python3-dcmstack all 0.9-1 [75.8 kB] Get: 154 http://deb.debian.org/debian unstable/main i386 python3-jsonpickle all 3.0.4+dfsg-1 [41.4 kB] Get: 155 http://deb.debian.org/debian unstable/main i386 python3-ordered-set all 4.1.0-1 [9628 B] Get: 156 http://deb.debian.org/debian unstable/main i386 python3-deepdiff all 6.7.1-2 [65.6 kB] Get: 157 http://deb.debian.org/debian unstable/main i386 python3-h5py-serial i386 3.10.0-1+b3 [1397 kB] Get: 158 http://deb.debian.org/debian unstable/main i386 python3-h5py all 3.10.0-1 [14.4 kB] Get: 159 http://deb.debian.org/debian unstable/main i386 python3-setuptools-scm all 8.0.4-2 [39.5 kB] Get: 160 http://deb.debian.org/debian unstable/main i386 python3-trx-python all 0.2.9-1 [40.2 kB] Get: 161 http://deb.debian.org/debian unstable/main i386 python3-tz all 2024.1-2 [30.9 kB] Get: 162 http://deb.debian.org/debian unstable/main i386 python3-pandas-lib i386 2.1.4+dfsg-8 [7491 kB] Get: 163 http://deb.debian.org/debian unstable/main i386 python3-pandas all 2.1.4+dfsg-8 [3015 kB] Get: 164 http://deb.debian.org/debian unstable/main i386 python3-dipy-lib i386 1.8.0-2 [3520 kB] Get: 165 http://deb.debian.org/debian unstable/main i386 python3-dipy all 1.8.0-2 [3458 kB] Get: 166 http://deb.debian.org/debian unstable/main i386 python3-duecredit all 0.9.1-1.1 [66.7 kB] Get: 167 http://deb.debian.org/debian unstable/main i386 python3-etelemetry all 0.3.1-1 [7244 B] Get: 168 http://deb.debian.org/debian unstable/main i386 python3-filelock all 3.14.0-1 [10.9 kB] Get: 169 http://deb.debian.org/debian unstable/main i386 python3-funcsigs all 1.0.2-5 [14.0 kB] Get: 170 http://deb.debian.org/debian unstable/main i386 python3-iniconfig all 1.1.1-2 [6396 B] Get: 171 http://deb.debian.org/debian unstable/main i386 python3-inotify all 0.2.10-5 [10.5 kB] Get: 172 http://deb.debian.org/debian unstable/main i386 python3-isodate all 0.6.1-2 [24.9 kB] Get: 173 http://deb.debian.org/debian unstable/main i386 python3-networkx all 3.2.1-4 [14.2 MB] Get: 174 http://deb.debian.org/debian unstable/main i386 python3-pyparsing all 3.1.2-1 [146 kB] Get: 175 http://deb.debian.org/debian unstable/main i386 python3-rdflib all 6.3.2-1 [395 kB] Get: 176 http://deb.debian.org/debian unstable/main i386 python3-prov all 2.0.0-2 [95.6 kB] Get: 177 http://deb.debian.org/debian unstable/main i386 python3-simplejson i386 3.19.2-1+b1 [70.7 kB] Get: 178 http://deb.debian.org/debian unstable/main i386 python3-traits i386 6.4.3-1 [4824 kB] Get: 179 http://deb.debian.org/debian unstable/main i386 python3-psutil i386 5.9.8-2 [226 kB] Get: 180 http://deb.debian.org/debian unstable/main i386 python3-nipype all 1.8.6-3 [1849 kB] Get: 181 http://deb.debian.org/debian unstable/main i386 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 182 http://deb.debian.org/debian unstable/main i386 python3-pytest all 8.1.2-1 [246 kB] Get: 183 http://deb.debian.org/debian unstable/main i386 python3-tinydb all 3.15.2-4 [20.8 kB] Fetched 156 MB in 4s (36.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19684 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-7_i386.deb ... Unpacking liblocale-gettext-perl (1.07-7) ... Selecting previously unselected package libpython3.11-minimal:i386. Preparing to unpack .../libpython3.11-minimal_3.11.9-1_i386.deb ... Unpacking libpython3.11-minimal:i386 (3.11.9-1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.6.2-1_i386.deb ... Unpacking libexpat1:i386 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_i386.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:i386 (3.11.9-1) ... Setting up libexpat1:i386 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20014 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_i386.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:i386. Preparing to unpack .../5-libreadline8t64_8.2-4_i386.deb ... Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:i386 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:i386. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_i386.deb ... Unpacking libpython3.11-stdlib:i386 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_i386.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21006 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_i386.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package libpython3.12-minimal:i386. Preparing to unpack .../001-libpython3.12-minimal_3.12.3-1_i386.deb ... Unpacking libpython3.12-minimal:i386 (3.12.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../002-python3.12-minimal_3.12.3-1_i386.deb ... Unpacking python3.12-minimal (3.12.3-1) ... Selecting previously unselected package libpopt0:i386. Preparing to unpack .../003-libpopt0_1.19+dfsg-1+b1_i386.deb ... Unpacking libpopt0:i386 (1.19+dfsg-1+b1) ... Selecting previously unselected package rsync. Preparing to unpack .../004-rsync_3.3.0-1_i386.deb ... Unpacking rsync (3.3.0-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../005-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package openssl. Preparing to unpack .../006-openssl_3.2.1-3_i386.deb ... Unpacking openssl (3.2.1-3) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../007-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../008-libmagic-mgc_1%3a5.45-3_i386.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:i386. Preparing to unpack .../009-libmagic1t64_1%3a5.45-3_i386.deb ... Unpacking libmagic1t64:i386 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../010-file_1%3a5.45-3_i386.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../011-gettext-base_0.21-14+b1_i386.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../012-libuchardet0_0.0.8-1+b1_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../013-groff-base_1.23.0-4_i386.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../014-bsdextrautils_2.40-8_i386.deb ... Unpacking bsdextrautils (2.40-8) ... 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Setting up libmagic1t64:i386 (1:5.45-3) ... Setting up libpython3.12-minimal:i386 (3.12.3-1) ... Setting up libpsl5t64:i386 (0.21.2-1.1) ... Setting up libnghttp2-14:i386 (1.61.0-1+b1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up 7zip (23.01+dfsg-12) ... Setting up libcom-err2:i386 (1.47.1~rc2-1) ... Setting up file (1:5.45-3) ... Setting up libturbojpeg0:i386 (1:2.1.5-3) ... Setting up libaec0:i386 (1.1.3-1) ... Setting up libelf1t64:i386 (0.191-1+b1) ... Setting up libkrb5support0:i386 (1.20.1-6+b1) ... Setting up libsasl2-modules-db:i386 (2.1.28+dfsg1-6) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Sun May 12 22:31:58 UTC 2024. Universal Time is now: Sun May 12 22:31:58 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up liberror-perl (0.17029-2) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:i386 (3.12.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up liblzf1:i386 (3.6-4+b1) ... Setting up autopoint (0.21-14) ... Setting up libk5crypto3:i386 (1.20.1-6+b1) ... Setting up libsasl2-2:i386 (2.1.28+dfsg1-6) ... Setting up libgfortran5:i386 (14-20240429-1) ... Setting up autoconf (2.71-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:i386 (0.0.8-1+b1) ... Setting up libopenjp2-7:i386 (2.5.0-2+b3) ... Setting up libsub-override-perl (0.10-1) ... Setting up git-man (1:2.43.0-1) ... Setting up netbase (6.4) ... Setting up libkrb5-3:i386 (1.20.1-6+b1) ... Setting up libssh2-1t64:i386 (1.11.0-4.1+b2) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up lsb-release (12.0-2) ... Setting up libfido2-1:i386 (1.14.0-1+b2) ... Setting up openssl (3.2.1-3) ... Setting up libbsd0:i386 (0.12.2-1) ... Setting up readline-common (8.2-4) ... Setting up libxml2:i386 (2.9.14+dfsg-1.3+b3) ... Setting up liblocale-gettext-perl (1.07-7) ... Setting up libsz2:i386 (1.1.3-1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libpopt0:i386 (1.19+dfsg-1+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up python3.12-minimal (3.12.3-1) ... Setting up liblapack3:i386 (3.12.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libedit2:i386 (3.1-20230828-1+b1) ... Setting up p7zip-full (16.02+transitional.1) ... Setting up dcm2niix (1.0.20220720-1+b1) ... Setting up libldap-2.5-0:i386 (2.5.17+dfsg-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libgssapi-krb5-2:i386 (1.20.1-6+b1) ... Setting up libjs-sphinxdoc (7.2.6-7) ... Setting up libreadline8t64:i386 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-4) ... Setting up libxslt1.1:i386 (1.1.35-1+b1) ... Setting up rsync (3.3.0-1) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up liblbfgsb0:i386 (3.0+dfsg.4-1+b1) ... Setting up libpython3.12-stdlib:i386 (3.12.3-1) ... Setting up libcurl4t64:i386 (8.7.1-5) ... Setting up openssh-client (1:9.7p1-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:i386 (3.11.9-1) ... Setting up python3.12 (3.12.3-1) ... Setting up libcurl3t64-gnutls:i386 (8.7.1-5) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up git (1:2.43.0-1+b1) ... Setting up curl (8.7.1-5) ... Setting up libhdf5-103-1t64:i386 (1.10.10+repack-3.3) ... Setting up libpython3-stdlib:i386 (3.11.8-1) ... Setting up libhdf5-hl-100t64:i386 (1.10.10+repack-3.3) ... Setting up python3.11 (3.11.9-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up python3-psutil (5.9.8-2) ... Setting up python3-tz (2024.1-2) ... Setting up python3-monotonic (1.6-2) ... Setting up python3-six (1.16.0-6) ... Setting up python3-simplejson (3.19.2-1+b1) ... Setting up python3-isodate (0.6.1-2) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (24.0-1) ... Setting up python3-iso8601 (1.0.2-1) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-certifi (2023.11.17-1) ... Setting up python3-funcsigs (1.0.2-5) ... Setting up python3-idna (3.6-2) ... Setting up python3-typing-extensions (4.10.0-1) ... Setting up python3-fasteners (0.18-2) ... Setting up python3-jeepney (0.8.0-3) ... Setting up python3-ci-info (0.3.0-1) ... Setting up python3-urllib3 (1.26.18-2) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-inotify (0.2.10-5) ... Setting up python3-lxml:i386 (5.2.1-1) ... Setting up python3-rdflib (6.3.2-1) ... Setting up git-annex (10.20240129-1+b1) ... Setting up python3-pydicom (2.4.3-1) ... Setting up python3-dateutil (2.9.0-2) ... Setting up python3-msgpack (1.0.3-3+b1) ... Setting up python3-lib2to3 (3.12.3-1) ... Setting up python3-appdirs (1.4.4-4) ... Setting up python3-cffi-backend:i386 (1.16.0-2+b2) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-1) ... python3.12: can't get files for byte-compilation Setting up python3-more-itertools (10.2.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-filelock (3.14.0-1) ... Setting up python3-jsonpickle (3.0.4+dfsg-1) ... Setting up python3-jaraco.classes (3.2.1-4) ... Setting up patool (2.0.0-2) ... Setting up python3-annexremote (1.6.4-2) ... Setting up python3-jaraco.functools (4.0.0-1) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-distro (1.9.0-1) ... Setting up python3-traits (6.4.3-1) ... Setting up python3-jaraco.context (4.3.0-1) ... Setting up python3-colorama (0.4.6-4) ... Setting up python3-citeproc (0.6.0-3) ... Setting up python3-charset-normalizer (3.3.2-1) ... Setting up python3-pytest (8.1.2-1) ... Setting up python3-pycryptodome (3.20.0+dfsg-1) ... Setting up python3-tqdm (4.66.4-1) ... Setting up python3-tinydb (3.15.2-4) ... Setting up python3-all (3.11.8-1) ... Setting up python3-ordered-set (4.1.0-1) ... Setting up python3-zipp (1.0.0-6) ... Setting up python3-click (8.1.7-1) ... Setting up python3-networkx (3.2.1-4) ... Setting up python3-setuptools-scm (8.0.4-2) ... Setting up python3-prov (2.0.0-2) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-cryptography (42.0.5-2) ... Setting up python3-requests (2.31.0+dfsg-1) ... Setting up python3-numpy (1:1.26.4+ds-8) ... Setting up python3-humanize (4.9.0-1) ... Setting up dh-python (6.20240422) ... Setting up python3-deepdiff (6.7.1-2) ... Setting up python3-scipy (1.11.4-6) ... Setting up python3-requests-toolbelt (1.0.0-2) ... Setting up python3-importlib-metadata (4.12.0-1) ... Setting up python3-duecredit (0.9.1-1.1) ... Setting up python3-pandas-lib:i386 (2.1.4+dfsg-8) ... Setting up python3-h5py-serial (3.10.0-1+b3) ... Setting up python3-etelemetry (0.3.1-1) ... Setting up python3-dipy-lib:i386 (1.8.0-2) ... Setting up python3-pandas (2.1.4+dfsg-8) ... Setting up python3-secretstorage (3.3.3-3) ... Setting up python3-nibabel (5.2.1-1) ... Setting up python3-h5py (3.10.0-1) ... Setting up python3-keyring (25.2.0-1) ... Setting up python3-gitlab (1:4.3.0-1) ... Setting up python3-trx-python (0.2.9-1) ... Setting up python3-dipy (1.8.0-2) ... /usr/lib/python3/dist-packages/dipy/reconst/qti.py:19: SyntaxWarning: invalid escape sequence '\m' """Convert symmetric 3 x 3 matrices into 6 x 1 vectors. /usr/lib/python3/dist-packages/dipy/reconst/qti.py:57: SyntaxWarning: invalid escape sequence '\m' """Convert 6 x 1 vectors into symmetric 3 x 3 matrices. /usr/lib/python3/dist-packages/dipy/reconst/qti.py:91: SyntaxWarning: invalid escape sequence '\m' """Convert symmetric 6 x 6 matrices into 21 x 1 vectors. /usr/lib/python3/dist-packages/dipy/reconst/qti.py:137: SyntaxWarning: invalid escape sequence '\m' """Convert 21 x 1 vectors into symmetric 6 x 6 matrices. /usr/lib/python3/dist-packages/dipy/reconst/qti.py:187: SyntaxWarning: invalid escape sequence '\m' """Convert a 1 x 6 vector into a symmetric 3 x 3 matrix. /usr/lib/python3/dist-packages/dipy/reconst/qti.py:222: SyntaxWarning: invalid escape sequence '\m' """Convert 1 x 21 vector into a symmetric 6 x 6 matrix. /usr/lib/python3/dist-packages/dipy/reconst/qti.py:280: SyntaxWarning: invalid escape sequence '\m' """Calculate covariance of a diffusion tensor distribution (DTD). /usr/lib/python3/dist-packages/dipy/reconst/qti.py:323: SyntaxWarning: invalid escape sequence '\e' """Generate signals using the covariance tensor signal representation. /usr/lib/python3/dist-packages/dipy/reconst/qti.py:395: SyntaxWarning: invalid escape sequence '\m' """Calculate the design matrix from the b-tensors. /usr/lib/python3/dist-packages/dipy/reconst/qti.py:761: SyntaxWarning: invalid escape sequence '\l' """Mean diffusivity. /usr/lib/python3/dist-packages/dipy/reconst/qti.py:783: SyntaxWarning: invalid escape sequence '\m' """Variance of microscopic mean diffusivities. /usr/lib/python3/dist-packages/dipy/reconst/qti.py:805: SyntaxWarning: invalid escape sequence '\m' """Shear variance. /usr/lib/python3/dist-packages/dipy/reconst/qti.py:827: SyntaxWarning: invalid escape sequence '\m' """Total isotropic variance. /usr/lib/python3/dist-packages/dipy/reconst/qti.py:863: SyntaxWarning: invalid escape sequence '\l' """Average of microscopic diffusion tensors' outer products with /usr/lib/python3/dist-packages/dipy/reconst/qti.py:886: SyntaxWarning: invalid escape sequence '\m' """Normalized variance of mean diffusivities. /usr/lib/python3/dist-packages/dipy/reconst/qti.py:909: SyntaxWarning: invalid escape sequence '\m' """Normalized microscopic anisotropy. /usr/lib/python3/dist-packages/dipy/reconst/qti.py:934: SyntaxWarning: invalid escape sequence '\m' """Microscopic fractional anisotropy. /usr/lib/python3/dist-packages/dipy/reconst/qti.py:953: SyntaxWarning: invalid escape sequence '\l' """Normalized macroscopic anisotropy. /usr/lib/python3/dist-packages/dipy/reconst/qti.py:979: SyntaxWarning: invalid escape sequence '\s' """Fractional anisotropy. /usr/lib/python3/dist-packages/dipy/reconst/qti.py:998: SyntaxWarning: invalid escape sequence '\m' """Microscopic orientation coherence. /usr/lib/python3/dist-packages/dipy/reconst/qti.py:1036: SyntaxWarning: invalid escape sequence '\m' """Bulk kurtosis. /usr/lib/python3/dist-packages/dipy/reconst/qti.py:1061: SyntaxWarning: invalid escape sequence '\m' """Shear kurtosis. /usr/lib/python3/dist-packages/dipy/reconst/qti.py:1086: SyntaxWarning: invalid escape sequence '\m' """Microscopic kurtosis. /usr/lib/python3/dist-packages/dipy/workflows/docstring_parser.py:308: SyntaxWarning: invalid escape sequence '\w' if re.compile('^([\w., ]+=)?\s*[\w\.]+\(.*\)$').match(summary_str): /usr/lib/python3/dist-packages/dipy/workflows/docstring_parser.py:352: SyntaxWarning: invalid escape sequence '\*' return [self['Signature'].replace('*', '\*')] + [''] Setting up python3-dcmstack (0.9-1) ... Setting up python3-keyrings.alt (5.0.1-1) ... Setting up python3-nipype (1.8.6-3) ... /usr/lib/python3/dist-packages/nipype/interfaces/io.py:1402: SyntaxWarning: invalid escape sequence '\w' field_name = re.match("\w+", field_name).group() /usr/lib/python3/dist-packages/nipype/interfaces/utility/base.py:232: SyntaxWarning: invalid escape sequence '\w' """Change the name of a file based on a mapped format string. Setting up python3-datalad (0.19.6-2) ... Processing triggers for libc-bin (2.38-11) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/heudiconv-1.1.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../heudiconv_1.1.1-1_source.changes dpkg-buildpackage: info: source package heudiconv dpkg-buildpackage: info: source version 1.1.1-1 dpkg-buildpackage: info: source distribution experimental dpkg-buildpackage: info: source changed by Alexandre Detiste dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild pybuild --clean -i python{version} -p "3.12 3.11" I: pybuild base:311: python3.12 setup.py clean running clean removing '/build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build' (and everything under it) 'build/bdist.linux-i686' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it I: pybuild base:311: python3.11 setup.py clean running clean removing '/build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build' (and everything under it) 'build/bdist.linux-i686' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it rm -rf .pybuild/ find . -name \*.pyc -exec rm {} \; dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/heudiconv.substvars debian/files rm -fr -- debian/heudiconv/ debian/tmp/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules execute_after_dh_clean make[1]: Entering directory '/build/reproducible-path/heudiconv-1.1.1' # Ahhhhhhh! rm -rf .pybuild build .pytest_cache/ rm -rf heudiconv.egg-info/ make[1]: Leaving directory '/build/reproducible-path/heudiconv-1.1.1' debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild pybuild --configure -i python{version} -p "3.12 3.11" I: pybuild base:311: python3.12 setup.py config running config I: pybuild base:311: python3.11 setup.py config running config dh_auto_build -O--buildsystem=pybuild pybuild --build -i python{version} -p "3.12 3.11" I: pybuild base:311: /usr/bin/python3.12 setup.py build running build running build_py creating /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv copying heudiconv/convert.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv copying heudiconv/info.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv copying heudiconv/parser.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv copying heudiconv/queue.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv copying heudiconv/main.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv copying heudiconv/_version.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv copying heudiconv/bids.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv copying heudiconv/__init__.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv copying heudiconv/utils.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv copying heudiconv/dicoms.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv copying heudiconv/due.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv creating /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests copying heudiconv/tests/test_regression.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests copying heudiconv/tests/anonymize_script.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests copying heudiconv/tests/test_bids.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests copying heudiconv/tests/test_utils.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests copying heudiconv/tests/__init__.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests copying heudiconv/tests/test_heuristics.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests copying heudiconv/tests/utils.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests copying heudiconv/tests/test_main.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests copying heudiconv/tests/conftest.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests copying heudiconv/tests/test_archives.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests copying heudiconv/tests/test_queue.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests copying heudiconv/tests/test_monitor.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests copying heudiconv/tests/test_dicoms.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests copying heudiconv/tests/test_convert.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests copying heudiconv/tests/test_tarballs.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests creating /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/external copying heudiconv/external/dlad.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/external copying heudiconv/external/__init__.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/external creating /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/cli copying heudiconv/cli/run.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/cli copying heudiconv/cli/__init__.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/cli copying heudiconv/cli/monitor.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/cli creating /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/heuristics copying heudiconv/heuristics/convertall_custom.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/heuristics copying heudiconv/heuristics/test_reproin.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/heuristics copying heudiconv/heuristics/studyforrest_phase2.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/heuristics copying heudiconv/heuristics/cmrr_heuristic.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/heuristics copying heudiconv/heuristics/convertall.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/heuristics copying heudiconv/heuristics/bids_PhoenixReport.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/heuristics copying heudiconv/heuristics/multires_7Tbold.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/heuristics copying heudiconv/heuristics/uc_bids.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/heuristics copying heudiconv/heuristics/example.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/heuristics copying heudiconv/heuristics/__init__.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/heuristics copying heudiconv/heuristics/test_b0dwi_for_fmap.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/heuristics copying heudiconv/heuristics/banda-bids.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/heuristics copying heudiconv/heuristics/bids_with_ses.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/heuristics copying heudiconv/heuristics/bids_ME.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/heuristics copying heudiconv/heuristics/reproin.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/heuristics creating /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/external/tests copying heudiconv/external/tests/__init__.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/external/tests copying heudiconv/external/tests/test_dlad.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/external/tests copying heudiconv/py.typed -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv creating /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests/data copying heudiconv/tests/data/phantom.dcm -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests/data copying heudiconv/tests/data/MRI_102TD_PHA_S.MR.Chen_Matthews_1.3.1.2022.11.16.15.50.20.357.31204541.dcm -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests/data copying heudiconv/tests/data/axasc35.dcm -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests/data creating /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests/data/b0dwiForFmap copying heudiconv/tests/data/b0dwiForFmap/b0dwi_for_fmap+00002.dcm -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests/data/b0dwiForFmap copying heudiconv/tests/data/b0dwiForFmap/b0dwi_for_fmap+00003.dcm -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests/data/b0dwiForFmap copying heudiconv/tests/data/b0dwiForFmap/b0dwi_for_fmap+00001.dcm -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests/data/b0dwiForFmap creating /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests/data/01-fmap_acq-3mm copying heudiconv/tests/data/01-fmap_acq-3mm/1.3.12.2.1107.5.2.43.66112.2016101409263663466202201.dcm -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests/data/01-fmap_acq-3mm creating /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests/data/01-anat-scout copying heudiconv/tests/data/01-anat-scout/0001.dcm -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests/data/01-anat-scout creating /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests/data/Phoenix creating /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests/data/Phoenix/99+PhoenixDocument copying heudiconv/tests/data/Phoenix/99+PhoenixDocument/99+PhoenixDocument+00001.dcm -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests/data/Phoenix/99+PhoenixDocument creating /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests/data/Phoenix/01+AA copying heudiconv/tests/data/Phoenix/01+AA/01+AA+00001.dcm -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests/data/Phoenix/01+AA copying heudiconv/tests/data/sample_nifti.nii.gz -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests/data copying heudiconv/tests/data/sample_nifti_params.txt -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests/data I: pybuild base:311: /usr/bin/python3 setup.py build running build running build_py creating /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv copying heudiconv/convert.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv copying heudiconv/info.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv copying heudiconv/parser.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv copying heudiconv/queue.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv copying heudiconv/main.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv copying heudiconv/_version.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv copying heudiconv/bids.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv copying heudiconv/__init__.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv copying heudiconv/utils.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv copying heudiconv/dicoms.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv copying heudiconv/due.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv creating /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests copying heudiconv/tests/test_regression.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests copying heudiconv/tests/anonymize_script.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests copying heudiconv/tests/test_bids.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests copying heudiconv/tests/test_utils.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests copying heudiconv/tests/__init__.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests copying heudiconv/tests/test_heuristics.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests copying heudiconv/tests/utils.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests copying heudiconv/tests/test_main.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests copying heudiconv/tests/conftest.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests copying heudiconv/tests/test_archives.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests copying heudiconv/tests/test_queue.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests copying heudiconv/tests/test_monitor.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests copying heudiconv/tests/test_dicoms.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests copying heudiconv/tests/test_convert.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests copying heudiconv/tests/test_tarballs.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests creating /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/external copying heudiconv/external/dlad.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/external copying heudiconv/external/__init__.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/external creating /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/cli copying heudiconv/cli/run.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/cli copying heudiconv/cli/__init__.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/cli copying heudiconv/cli/monitor.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/cli creating /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/heuristics copying heudiconv/heuristics/convertall_custom.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/heuristics copying heudiconv/heuristics/test_reproin.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/heuristics copying heudiconv/heuristics/studyforrest_phase2.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/heuristics copying heudiconv/heuristics/cmrr_heuristic.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/heuristics copying heudiconv/heuristics/convertall.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/heuristics copying heudiconv/heuristics/bids_PhoenixReport.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/heuristics copying heudiconv/heuristics/multires_7Tbold.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/heuristics copying heudiconv/heuristics/uc_bids.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/heuristics copying heudiconv/heuristics/example.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/heuristics copying heudiconv/heuristics/__init__.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/heuristics copying heudiconv/heuristics/test_b0dwi_for_fmap.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/heuristics copying heudiconv/heuristics/banda-bids.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/heuristics copying heudiconv/heuristics/bids_with_ses.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/heuristics copying heudiconv/heuristics/bids_ME.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/heuristics copying heudiconv/heuristics/reproin.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/heuristics creating /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/external/tests copying heudiconv/external/tests/__init__.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/external/tests copying heudiconv/external/tests/test_dlad.py -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/external/tests copying heudiconv/py.typed -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv creating /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests/data copying heudiconv/tests/data/phantom.dcm -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests/data copying heudiconv/tests/data/MRI_102TD_PHA_S.MR.Chen_Matthews_1.3.1.2022.11.16.15.50.20.357.31204541.dcm -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests/data copying heudiconv/tests/data/axasc35.dcm -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests/data creating /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests/data/b0dwiForFmap copying heudiconv/tests/data/b0dwiForFmap/b0dwi_for_fmap+00002.dcm -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests/data/b0dwiForFmap copying heudiconv/tests/data/b0dwiForFmap/b0dwi_for_fmap+00003.dcm -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests/data/b0dwiForFmap copying heudiconv/tests/data/b0dwiForFmap/b0dwi_for_fmap+00001.dcm -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests/data/b0dwiForFmap creating /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests/data/01-fmap_acq-3mm copying heudiconv/tests/data/01-fmap_acq-3mm/1.3.12.2.1107.5.2.43.66112.2016101409263663466202201.dcm -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests/data/01-fmap_acq-3mm creating /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests/data/01-anat-scout copying heudiconv/tests/data/01-anat-scout/0001.dcm -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests/data/01-anat-scout creating /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests/data/Phoenix creating /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests/data/Phoenix/99+PhoenixDocument copying heudiconv/tests/data/Phoenix/99+PhoenixDocument/99+PhoenixDocument+00001.dcm -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests/data/Phoenix/99+PhoenixDocument creating /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests/data/Phoenix/01+AA copying heudiconv/tests/data/Phoenix/01+AA/01+AA+00001.dcm -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests/data/Phoenix/01+AA copying heudiconv/tests/data/sample_nifti.nii.gz -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests/data copying heudiconv/tests/data/sample_nifti_params.txt -> /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests/data dh_auto_test -O--buildsystem=pybuild pybuild --test --test-pytest -i python{version} -p "3.12 3.11" I: pybuild pybuild:308: cp -a heudiconv/tests /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/ I: pybuild base:311: cd /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build; python3.12 -m pytest heudiconv/tests/test_* -k 'not test_bvals_are_zero' ============================= test session starts ============================== platform linux -- Python 3.12.3, pytest-8.1.2, pluggy-1.5.0 rootdir: /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build configfile: pyproject.toml collected 116 items / 1 deselected / 115 selected heudiconv/tests/test_archives.py .......... [ 8%] heudiconv/tests/test_bids.py ..................................s. [ 40%] heudiconv/tests/test_convert.py .......... [ 48%] heudiconv/tests/test_dicoms.py .........ss [ 58%] heudiconv/tests/test_heuristics.py .F......... [ 67%] heudiconv/tests/test_main.py .............. [ 80%] heudiconv/tests/test_monitor.py ssss [ 83%] heudiconv/tests/test_queue.py ... [ 86%] heudiconv/tests/test_regression.py sss. [ 89%] heudiconv/tests/test_tarballs.py . [ 90%] heudiconv/tests/test_utils.py ........... [100%] =================================== FAILURES =================================== _______________ test_reproin_largely_smoke[invocation0-reproin] ________________ tmp_path = PosixPath('/tmp/pytest-of-pbuilder1/pytest-0/test_reproin_largely_smoke_inv0') heuristic = 'reproin' invocation = ['--files', '/build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests/data'] @pytest.mark.parametrize("heuristic", ["reproin", "convertall"]) @pytest.mark.parametrize( "invocation", [ ["--files", TESTS_DATA_PATH], # our new way with automated grouping ["-d", f"{TESTS_DATA_PATH}/{{subject}}/*", "-s", "01-fmap_acq-3mm"], # "old" way specifying subject # should produce the same results ], ) @pytest.mark.skipif(Dataset is None, reason="no datalad") def test_reproin_largely_smoke(tmp_path: Path, heuristic: str, invocation: str) -> None: is_bids = True if heuristic == "reproin" else False args = [ "--random-seed", "1", "-f", heuristic, "-c", "dcm2niix", "-o", str(tmp_path), ] if is_bids: args.append("-b") args.append("--datalad") args.extend(invocation) # Test some safeguards if invocation[0] == "--files": # Multiple subjects must not be specified -- only a single one could # be overridden from the command line with pytest.raises(ValueError): runner(args + ["--subjects", "sub1", "sub2"]) if heuristic != "reproin": # if subject is not overridden, raise error with pytest.raises(NotImplementedError): runner(args) return runner(args) ds = Dataset(tmp_path) assert ds.is_installed() assert not ds.repo.dirty head = ds.repo.get_hexsha() # and if we rerun -- should fail lgr.info( "RERUNNING, expecting to FAIL since the same everything " "and -c specified so we did conversion already" ) with pytest.raises(RuntimeError): runner(args) # but there should be nothing new assert not ds.repo.dirty # TODO: remove whenever https://github.com/datalad/datalad/issues/6843 # is fixed/released buggy_datalad = (ds.pathobj / ".gitmodules").read_text().splitlines().count( '[submodule "Halchenko"]' ) > 1 assert head == ds.repo.get_hexsha() or buggy_datalad # unless we pass 'overwrite' flag > runner(args + ["--overwrite"]) heudiconv/tests/test_heuristics.py:120: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ heudiconv/cli/run.py:30: in main workflow(**kwargs) heudiconv/main.py:410: in workflow study_sessions = get_study_sessions( heudiconv/parser.py:221: in get_study_sessions seqinfo_dict = group_dicoms_into_seqinfos( heudiconv/dicoms.py:324: in group_dicoms_into_seqinfos mwinfo = validate_dicom(filename, dcmfilter) heudiconv/dicoms.py:157: in validate_dicom mw = dw.wrapper_from_file(fl, force=True, stop_before_pixels=True) /usr/lib/python3/dist-packages/nibabel/nicom/dicomwrappers.py:58: in wrapper_from_file dcm_data = pydicom.dcmread(fobj, *args, **kwargs) /usr/lib/python3/dist-packages/pydicom/filereader.py:1030: in dcmread dataset = read_partial( /usr/lib/python3/dist-packages/pydicom/filereader.py:852: in read_partial dataset = read_dataset( /usr/lib/python3/dist-packages/pydicom/filereader.py:427: in read_dataset raw_data_element = next(de_gen) /usr/lib/python3/dist-packages/pydicom/filereader.py:207: in data_element_generator fp_read(length) if length > 0 _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = , size = 1768444706 def read(self, size: int = -1, /) -> bytes: > return self.fobj.read(size) E MemoryError /usr/lib/python3/dist-packages/nibabel/openers.py:223: MemoryError ----------------------------- Captured stdout call ----------------------------- create(ok): /tmp/pytest-of-pbuilder1/pytest-0/test_reproin_largely_smoke_inv0 (dataset) add(ok): head (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): head (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): advanced applications libraries (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): advanced applications libraries (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): .gitattributes (file) save(ok): . (dataset) action summary: add (ok: 1) save (ok: 1) add(ok): advanced applications libraries (dataset) add(ok): .gitmodules (file) save(ok): head (dataset) add(ok): head (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) action summary: add (ok: 4) save (notneeded: 1, ok: 2) add(ok): .heudiconv (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): .heudiconv (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): dbictest1/info/dbictest1.auto.txt (file) add(ok): dbictest1/info/dbictest1.edit.txt (file) add(ok): dbictest1/info/dicominfo.tsv (file) add(ok): dbictest1/info/filegroup.json (file) add(ok): dbictest1/info/heuristic.py (file) save(ok): .heudiconv (dataset) add(ok): .heudiconv (dataset) add(ok): .gitmodules (file) add(ok): .bidsignore (file) add(ok): .gitignore (file) add(ok): CHANGES (file) add(ok): README (file) add(ok): dataset_description.json (file) add(ok): participants.json (file) add(ok): participants.tsv (file) add(ok): scans.json (file) add(ok): sourcedata/README (file) add(ok): sourcedata/sub-dbictest1/anat/sub-dbictest1_scout.dicom.tgz (file) save(ok): . (dataset) action summary: add (ok: 17) save (ok: 2) add(ok): advanced applications libraries (dataset) add(ok): .gitmodules (file) save(ok): head (dataset) add(ok): head (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) action summary: add (ok: 4) save (notneeded: 2, ok: 2) add(ok): Development (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): Development (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): Functional (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): Functional (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): .gitattributes (file) save(ok): . (dataset) action summary: add (ok: 1) save (ok: 1) add(ok): Functional (dataset) add(ok): .gitmodules (file) save(ok): Development (dataset) add(ok): Development (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) action summary: add (ok: 4) save (notneeded: 1, ok: 2) add(ok): .heudiconv (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): .heudiconv (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): o6jgilro/info/dicominfo.tsv (file) add(ok): o6jgilro/info/filegroup.json (file) add(ok): o6jgilro/info/heuristic.py (file) add(ok): o6jgilro/info/o6jgilro.auto.txt (file) add(ok): o6jgilro/info/o6jgilro.edit.txt (file) save(ok): .heudiconv (dataset) add(ok): .heudiconv (dataset) add(ok): .gitmodules (file) add(ok): .bidsignore (file) add(ok): .gitignore (file) add(ok): CHANGES (file) add(ok): README (file) add(ok): dataset_description.json (file) add(ok): participants.json (file) add(ok): participants.tsv (file) add(ok): scans.json (file) add(ok): sourcedata/README (file) add(ok): sourcedata/sub-o6jgilro/anat/sub-o6jgilro_32ch-head-coil_scout.dicom.tgz (file) save(ok): . (dataset) action summary: add (ok: 17) save (ok: 2) add(ok): Functional (dataset) add(ok): .gitmodules (file) save(ok): Development (dataset) add(ok): Development (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) action summary: add (ok: 4) save (notneeded: 2, ok: 2) add(ok): Halchenko (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): Halchenko (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): Yarik (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): Yarik (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): 950_bids_test4 (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): 950_bids_test4 (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): .gitattributes (file) save(ok): . (dataset) action summary: add (ok: 1) save (ok: 1) add(ok): 950_bids_test4 (dataset) add(ok): .gitmodules (file) save(ok): Halchenko/Yarik (dataset) add(ok): Yarik (dataset) add(ok): .gitmodules (file) save(ok): Halchenko (dataset) add(ok): Halchenko (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) action summary: add (ok: 6) save (notneeded: 1, ok: 3) 240512-10:34:15,799 nipype.workflow INFO: [Node] Setting-up "convert" in "/tmp/dcm2niix_0u0yev1/convert". 240512-10:34:15,803 nipype.workflow INFO: [Node] Executing "convert" 240512-10:34:15,832 nipype.interface INFO: stdout 2024-05-12T10:34:15.832070:Chris Rorden's dcm2niiX version v1.0.20220720 (JP2:OpenJPEG) GCC13.2.0 (32-bit Linux) 240512-10:34:15,832 nipype.interface INFO: stdout 2024-05-12T10:34:15.832070:Found 1 DICOM file(s) 240512-10:34:15,832 nipype.interface INFO: stdout 2024-05-12T10:34:15.832070:Convert 1 DICOM as /tmp/pytest-of-pbuilder1/pytest-0/test_reproin_largely_smoke_inv0/Halchenko/Yarik/950_bids_test4/sub-phantom1sid1/ses-localizer/fmap/sub-phantom1sid1_ses-localizer_acq-3mm_phasediff_heudiconv137_e2_ph (64x64x1x1) 240512-10:34:15,833 nipype.interface INFO: stdout 2024-05-12T10:34:15.833039:Conversion required 0.008534 seconds (0.008224 for core code). 240512-10:34:15,888 nipype.workflow INFO: [Node] Finished "convert", elapsed time 0.08356s. 240512-10:34:15,915 nipype.workflow INFO: [Node] Setting-up "embedder" in "/tmp/embedmetaqtuj4kkm/embedder". 240512-10:34:15,920 nipype.workflow INFO: [Node] Executing "embedder" 240512-10:34:15,972 nipype.workflow INFO: [Node] Finished "embedder", elapsed time 0.050316s. add(ok): .heudiconv (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): .heudiconv (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): phantom1sid1/ses-localizer/info/dicominfo_ses-localizer.tsv (file) add(ok): phantom1sid1/ses-localizer/info/filegroup_ses-localizer.json (file) add(ok): phantom1sid1/ses-localizer/info/heuristic.py (file) add(ok): phantom1sid1/ses-localizer/info/phantom1sid1_ses-localizer.auto.txt (file) add(ok): phantom1sid1/ses-localizer/info/phantom1sid1_ses-localizer.edit.txt (file) save(ok): .heudiconv (dataset) add(ok): .heudiconv (dataset) add(ok): .gitmodules (file) add(ok): .bidsignore (file) add(ok): .gitignore (file) add(ok): CHANGES (file) add(ok): README (file) add(ok): dataset_description.json (file) add(ok): participants.json (file) add(ok): participants.tsv (file) add(ok): scans.json (file) add(ok): sourcedata/README (file) add(ok): sourcedata/sub-phantom1sid1/ses-localizer/anat/sub-phantom1sid1_ses-localizer_scout.dicom.tgz (file) add(ok): sourcedata/sub-phantom1sid1/ses-localizer/fmap/sub-phantom1sid1_ses-localizer_acq-3mm_phasediff.dicom.tgz (file) add(ok): sub-phantom1sid1/ses-localizer/fmap/sub-phantom1sid1_ses-localizer_acq-3mm_phasediff.json (file) add(ok): sub-phantom1sid1/ses-localizer/fmap/sub-phantom1sid1_ses-localizer_acq-3mm_phasediff.nii.gz (file) add(ok): sub-phantom1sid1/ses-localizer/sub-phantom1sid1_ses-localizer_scans.tsv (file) save(ok): . (dataset) action summary: add (ok: 21) save (ok: 2) add(ok): 950_bids_test4 (dataset) add(ok): .gitmodules (file) save(ok): Halchenko/Yarik (dataset) add(ok): Yarik (dataset) add(ok): .gitmodules (file) save(ok): Halchenko (dataset) add(ok): Halchenko (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) action summary: add (ok: 6) save (notneeded: 2, ok: 3) add(ok): Chen (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): Chen (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): Matthews (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): Matthews (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): 102TD_Development (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): 102TD_Development (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): .gitattributes (file) save(ok): . (dataset) action summary: add (ok: 1) save (ok: 1) add(ok): 102TD_Development (dataset) add(ok): .gitmodules (file) save(ok): Chen/Matthews (dataset) add(ok): Matthews (dataset) add(ok): .gitmodules (file) save(ok): Chen (dataset) add(ok): Chen (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) action summary: add (ok: 6) save (notneeded: 1, ok: 3) add(ok): .heudiconv (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): .heudiconv (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): phasmr6335/info/dicominfo.tsv (file) add(ok): phasmr6335/info/filegroup.json (file) add(ok): phasmr6335/info/heuristic.py (file) add(ok): phasmr6335/info/phasmr6335.auto.txt (file) add(ok): phasmr6335/info/phasmr6335.edit.txt (file) save(ok): .heudiconv (dataset) add(ok): .heudiconv (dataset) add(ok): .gitmodules (file) add(ok): .bidsignore (file) add(ok): .gitignore (file) add(ok): CHANGES (file) add(ok): README (file) add(ok): dataset_description.json (file) add(ok): participants.json (file) add(ok): participants.tsv (file) add(ok): scans.json (file) add(ok): sourcedata/README (file) add(ok): sourcedata/sub-phasmr6335/anat/sub-phasmr6335_scout.dicom.tgz (file) save(ok): . (dataset) action summary: add (ok: 17) save (ok: 2) add(ok): 102TD_Development (dataset) add(ok): .gitmodules (file) save(ok): Chen/Matthews (dataset) add(ok): Matthews (dataset) add(ok): .gitmodules (file) save(ok): Chen (dataset) add(ok): Chen (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) action summary: add (ok: 6) save (notneeded: 2, ok: 3) add(ok): Research (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): Research (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): MCBI_TESTING (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): MCBI_TESTING (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): .gitattributes (file) save(ok): . (dataset) action summary: add (ok: 1) save (ok: 1) add(ok): MCBI_TESTING (dataset) add(ok): .gitmodules (file) save(ok): Research (dataset) add(ok): Research (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) action summary: add (ok: 4) save (notneeded: 1, ok: 2) add(ok): .heudiconv (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): .heudiconv (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): crlab/info/crlab.auto.txt (file) add(ok): crlab/info/crlab.edit.txt (file) add(ok): crlab/info/dicominfo.tsv (file) add(ok): crlab/info/filegroup.json (file) add(ok): crlab/info/heuristic.py (file) save(ok): .heudiconv (dataset) add(ok): .heudiconv (dataset) add(ok): .gitmodules (file) add(ok): .bidsignore (file) add(ok): .gitignore (file) add(ok): CHANGES (file) add(ok): README (file) add(ok): dataset_description.json (file) add(ok): participants.json (file) add(ok): participants.tsv (file) add(ok): scans.json (file) save(ok): . (dataset) action summary: add (ok: 15) save (ok: 2) add(ok): MCBI_TESTING (dataset) add(ok): .gitmodules (file) save(ok): Research (dataset) add(ok): Research (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) action summary: add (ok: 4) save (notneeded: 2, ok: 2) add(ok): Investigators (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): Investigators (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): Winawer (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): Winawer (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): .gitattributes (file) save(ok): . (dataset) action summary: add (ok: 1) save (ok: 1) add(ok): Winawer (dataset) add(ok): .gitmodules (file) save(ok): Investigators (dataset) add(ok): Investigators (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) action summary: add (ok: 4) save (notneeded: 1, ok: 2) add(ok): .heudiconv (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): .heudiconv (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): ke6hl9lm/info/dicominfo.tsv (file) add(ok): ke6hl9lm/info/filegroup.json (file) add(ok): ke6hl9lm/info/heuristic.py (file) add(ok): ke6hl9lm/info/ke6hl9lm.auto.txt (file) add(ok): ke6hl9lm/info/ke6hl9lm.edit.txt (file) save(ok): .heudiconv (dataset) add(ok): .heudiconv (dataset) add(ok): .gitmodules (file) add(ok): .bidsignore (file) add(ok): .gitignore (file) add(ok): CHANGES (file) add(ok): README (file) add(ok): dataset_description.json (file) add(ok): participants.json (file) add(ok): participants.tsv (file) add(ok): scans.json (file) save(ok): . (dataset) action summary: add (ok: 15) save (ok: 2) add(ok): Winawer (dataset) add(ok): .gitmodules (file) save(ok): Investigators (dataset) add(ok): Investigators (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) action summary: add (ok: 4) save (notneeded: 2, ok: 2) action summary: save (notneeded: 2) add(ok): head (dataset) add(ok): .gitmodules (file) action summary: add (ok: 2) save (notneeded: 4) action summary: save (notneeded: 2) add(ok): Development (dataset) add(ok): .gitmodules (file) action summary: add (ok: 2) save (notneeded: 4) ------------------------------ Captured log call ------------------------------- WARNING heudiconv.main:main.py:362 Could not check for version updates: Connection to server could not be made WARNING heudiconv.dicoms:dicoms.py:176 Ignoring /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests/data/sample_nifti.json since not quite a "normal" DICOM: 'FileDataset' object has no attribute 'SeriesNumber' WARNING heudiconv.dicoms:dicoms.py:176 Ignoring /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests/data/sample_nifti.nii.gz since not quite a "normal" DICOM: 'FileDataset' object has no attribute 'SeriesNumber' WARNING heudiconv.dicoms:dicoms.py:176 Ignoring /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests/data/sample_nifti_params.txt since not quite a "normal" DICOM: 'FileDataset' object has no attribute 'SeriesNumber' INFO datalad:log.py:432 Clear progress bars INFO datalad:log.py:432 Refresh progress bars INFO datalad.core.local.save:log.py:432 Total: starting INFO datalad.core.local.save:log.py:432 INFO datalad:log.py:432 Clear progress bars INFO datalad:log.py:432 Refresh progress bars INFO datalad:log.py:432 Clear progress bars INFO datalad:log.py:432 Refresh progress bars INFO datalad.core.local.save:log.py:432 Total: processed result for /tmp/pytest-of-pbuilder1/pytest-0/test_reproin_largely_smoke_inv0 INFO datalad:log.py:432 Clear progress bars INFO datalad:log.py:432 Refresh progress bars INFO datalad.core.local.save:log.py:432 Total: done INFO datalad:log.py:432 Clear progress bars 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datalad.core.local.save:log.py:432 Total: processed result for /tmp/pytest-of-pbuilder1/pytest-0/test_reproin_largely_smoke_inv0/Development/Functional INFO datalad:log.py:432 Clear progress bars INFO datalad:log.py:432 Refresh progress bars INFO datalad.core.local.save:log.py:432 Total: done INFO datalad:log.py:432 Clear progress bars INFO datalad:log.py:432 Refresh progress bars INFO datalad.core.local.save:log.py:432 Total: starting INFO datalad.core.local.save:log.py:432 INFO datalad.core.local.save:log.py:432 Total: processed result for /tmp/pytest-of-pbuilder1/pytest-0/test_reproin_largely_smoke_inv0/Development/Functional INFO datalad.core.local.save:log.py:432 Total: done INFO datalad.core.local.save:log.py:432 Total: starting INFO datalad.core.local.save:log.py:432 INFO datalad.core.local.save:log.py:432 Total: processed result for /tmp/pytest-of-pbuilder1/pytest-0/test_reproin_largely_smoke_inv0/Development/Functional INFO datalad:log.py:432 Clear progress bars INFO datalad:log.py:432 Refresh progress bars INFO datalad:log.py:432 Clear progress bars INFO datalad:log.py:432 Refresh progress bars INFO datalad.core.local.save:log.py:432 Total: processed result for /tmp/pytest-of-pbuilder1/pytest-0/test_reproin_largely_smoke_inv0/Development INFO datalad:log.py:432 Clear progress bars INFO datalad:log.py:432 Refresh progress bars INFO datalad:log.py:432 Clear progress bars INFO datalad:log.py:432 Refresh progress bars INFO datalad:log.py:432 Clear progress bars INFO datalad:log.py:432 Refresh progress bars INFO datalad.core.local.save:log.py:432 Total: processed result for /tmp/pytest-of-pbuilder1/pytest-0/test_reproin_largely_smoke_inv0 INFO datalad:log.py:432 Clear progress bars INFO datalad:log.py:432 Refresh progress bars INFO datalad.core.local.save:log.py:432 Total: done INFO datalad:log.py:432 Clear progress bars INFO datalad:log.py:432 Refresh progress bars WARNING heudiconv:reproin.py:456 Could not determine the series name by looking at protocol_name, series_description fields WARNING heudiconv:reproin.py:662 Could not figure out where to stick 1 sequences: ['99-Phoenix Document'] WARNING heudiconv.bids:bids.py:1025 We cannot add the IntendedFor field: no fmap/ in /tmp/pytest-of-pbuilder1/pytest-0/test_reproin_largely_smoke_inv0/Development/Functional/sub-o6jgilro INFO datalad.core.local.save:log.py:432 Total: starting INFO datalad.core.local.save:log.py:432 INFO datalad.core.local.save:log.py:432 Total: processed result for /tmp/pytest-of-pbuilder1/pytest-0/test_reproin_largely_smoke_inv0/Development/Functional INFO datalad.core.local.save:log.py:432 Total: done INFO datalad.core.local.save:log.py:432 Total: starting INFO datalad.core.local.save:log.py:432 INFO datalad:log.py:432 Clear progress bars INFO datalad:log.py:432 Refresh progress bars INFO datalad:log.py:432 Clear progress bars INFO datalad:log.py:432 Refresh progress bars INFO datalad.core.local.save:log.py:432 Total: processed result for 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Setting-up "convert" in "/tmp/dcm2niix_0u0yev1/convert". INFO nipype.workflow:nodes.py:716 [Node] Executing "convert" INFO nipype.interface:subprocess.py:69 stdout 2024-05-12T10:34:15.832070:Chris Rorden's dcm2niiX version v1.0.20220720 (JP2:OpenJPEG) GCC13.2.0 (32-bit Linux) INFO nipype.interface:subprocess.py:69 stdout 2024-05-12T10:34:15.832070:Found 1 DICOM file(s) INFO nipype.interface:subprocess.py:69 stdout 2024-05-12T10:34:15.832070:Convert 1 DICOM as /tmp/pytest-of-pbuilder1/pytest-0/test_reproin_largely_smoke_inv0/Halchenko/Yarik/950_bids_test4/sub-phantom1sid1/ses-localizer/fmap/sub-phantom1sid1_ses-localizer_acq-3mm_phasediff_heudiconv137_e2_ph (64x64x1x1) INFO nipype.interface:subprocess.py:69 stdout 2024-05-12T10:34:15.833039:Conversion required 0.008534 seconds (0.008224 for core code). INFO nipype.workflow:nodes.py:723 [Node] Finished "convert", elapsed time 0.08356s. INFO nipype.workflow:nodes.py:453 [Node] Setting-up "embedder" in "/tmp/embedmetaqtuj4kkm/embedder". INFO nipype.workflow:nodes.py:716 [Node] Executing "embedder" INFO nipype.workflow:nodes.py:723 [Node] Finished "embedder", elapsed time 0.050316s. 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not quite a "normal" DICOM: 'FileDataset' object has no attribute 'SeriesNumber' WARNING heudiconv.dicoms:dicoms.py:176 Ignoring /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests/data/sample_nifti.nii.gz since not quite a "normal" DICOM: 'FileDataset' object has no attribute 'SeriesNumber' WARNING heudiconv.dicoms:dicoms.py:176 Ignoring /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build/heudiconv/tests/data/sample_nifti_params.txt since not quite a "normal" DICOM: 'FileDataset' object has no attribute 'SeriesNumber' WARNING heudiconv.bids:bids.py:1025 We cannot add the IntendedFor field: no fmap/ in /tmp/pytest-of-pbuilder1/pytest-0/test_reproin_largely_smoke_inv0/head/advanced applications libraries/sub-dbictest1 INFO datalad.core.local.save:log.py:432 Total: starting INFO datalad.core.local.save:log.py:432 INFO datalad.core.local.save:log.py:432 Total: processed result for 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applications libraries/.heudiconv INFO datalad.core.local.save:log.py:432 Total: processed result for /tmp/pytest-of-pbuilder1/pytest-0/test_reproin_largely_smoke_inv0/head/advanced applications libraries INFO datalad.core.local.save:log.py:432 Total: processed result for /tmp/pytest-of-pbuilder1/pytest-0/test_reproin_largely_smoke_inv0/head INFO datalad:log.py:432 Clear progress bars INFO datalad:log.py:432 Refresh progress bars INFO datalad:log.py:432 Clear progress bars INFO datalad:log.py:432 Refresh progress bars INFO datalad.core.local.save:log.py:432 Total: processed result for /tmp/pytest-of-pbuilder1/pytest-0/test_reproin_largely_smoke_inv0 INFO datalad.core.local.save:log.py:432 Total: done INFO datalad:log.py:432 Clear progress bars INFO datalad:log.py:432 Refresh progress bars WARNING heudiconv.bids:bids.py:1025 We cannot add the IntendedFor field: no fmap/ in /tmp/pytest-of-pbuilder1/pytest-0/test_reproin_largely_smoke_inv0/Development/Functional/sub-o6jgilro INFO datalad.core.local.save:log.py:432 Total: starting INFO datalad.core.local.save:log.py:432 INFO datalad.core.local.save:log.py:432 Total: processed result for /tmp/pytest-of-pbuilder1/pytest-0/test_reproin_largely_smoke_inv0/Development/Functional INFO datalad.core.local.save:log.py:432 Total: done INFO datalad.core.local.save:log.py:432 Total: starting INFO datalad.core.local.save:log.py:432 INFO datalad.core.local.save:log.py:432 Total: processed result for /tmp/pytest-of-pbuilder1/pytest-0/test_reproin_largely_smoke_inv0/Development/Functional/.heudiconv INFO datalad.core.local.save:log.py:432 Total: processed result for /tmp/pytest-of-pbuilder1/pytest-0/test_reproin_largely_smoke_inv0/Development/Functional INFO datalad.core.local.save:log.py:432 Total: done INFO datalad:log.py:432 Clear progress bars INFO datalad:log.py:432 Refresh progress bars INFO datalad.core.local.save:log.py:432 Total: starting INFO datalad.core.local.save:log.py:432 INFO datalad.core.local.save:log.py:432 Total: processed result for /tmp/pytest-of-pbuilder1/pytest-0/test_reproin_largely_smoke_inv0/Development/Functional/.heudiconv INFO datalad.core.local.save:log.py:432 Total: processed result for /tmp/pytest-of-pbuilder1/pytest-0/test_reproin_largely_smoke_inv0/Development/Functional INFO datalad.core.local.save:log.py:432 Total: processed result for /tmp/pytest-of-pbuilder1/pytest-0/test_reproin_largely_smoke_inv0/Development INFO datalad:log.py:432 Clear progress bars INFO datalad:log.py:432 Refresh progress bars INFO datalad:log.py:432 Clear progress bars INFO datalad:log.py:432 Refresh progress bars INFO datalad.core.local.save:log.py:432 Total: processed result for /tmp/pytest-of-pbuilder1/pytest-0/test_reproin_largely_smoke_inv0 INFO datalad.core.local.save:log.py:432 Total: done INFO datalad:log.py:432 Clear progress bars INFO datalad:log.py:432 Refresh progress bars WARNING heudiconv.main:main.py:362 Could not check for version updates: Connection to server could not be made =============================== warnings summary =============================== ../../../../../../usr/lib/python3/dist-packages/traits/observation/_generated_parser.py:258 /usr/lib/python3/dist-packages/traits/observation/_generated_parser.py:258: DeprecationWarning: module 'sre_parse' is deprecated import sre_parse ../../../../../../usr/lib/python3/dist-packages/traits/observation/_generated_parser.py:259 /usr/lib/python3/dist-packages/traits/observation/_generated_parser.py:259: DeprecationWarning: module 'sre_constants' is deprecated import sre_constants heudiconv/tests/test_archives.py::test_get_extracted_dicoms_single_session_is_none heudiconv/tests/test_archives.py::test_get_extracted_dicoms_multple_session_integers heudiconv/tests/test_archives.py::test_get_extracted_dicoms_multple_session_integers heudiconv/tests/test_archives.py::test_get_extracted_dicoms_from_archives[tar] heudiconv/tests/test_archives.py::test_get_extracted_dicoms_from_archives[gztar] heudiconv/tests/test_archives.py::test_get_extracted_dicoms_from_archives[bztar] heudiconv/tests/test_archives.py::test_get_extracted_dicoms_from_archives[xztar] heudiconv/tests/test_archives.py::test_get_extracted_dicoms_from_mixed_list /usr/lib/python3.12/tarfile.py:2221: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior. warnings.warn( heudiconv/tests/test_convert.py: 5 warnings heudiconv/tests/test_dicoms.py: 1 warning heudiconv/tests/test_heuristics.py: 18 warnings heudiconv/tests/test_main.py: 1 warning heudiconv/tests/test_regression.py: 2 warnings /usr/lib/python3/dist-packages/nipype/interfaces/base/support.py:76: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC). self._runtime.startTime = dt.isoformat(dt.utcnow()) heudiconv/tests/test_convert.py::test_b0dwi_for_fmap heudiconv/tests/test_convert.py::test_b0dwi_for_fmap /usr/lib/python3/dist-packages/nipype/utils/filemanip.py:696: DeprecationWarning: 'locale.getdefaultlocale' is deprecated and slated for removal in Python 3.15. Use setlocale(), getencoding() and getlocale() instead. default_encoding = encoding or locale.getdefaultlocale()[1] or "UTF-8" heudiconv/tests/test_convert.py: 5 warnings heudiconv/tests/test_dicoms.py: 1 warning heudiconv/tests/test_heuristics.py: 18 warnings heudiconv/tests/test_main.py: 1 warning heudiconv/tests/test_regression.py: 2 warnings /usr/lib/python3/dist-packages/nipype/interfaces/base/support.py:84: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC). self._runtime.endTime = dt.isoformat(dt.utcnow()) heudiconv/tests/test_convert.py: 4 warnings heudiconv/tests/test_dicoms.py: 2 warnings heudiconv/tests/test_heuristics.py: 20 warnings heudiconv/tests/test_main.py: 2 warnings heudiconv/tests/test_regression.py: 4 warnings /usr/lib/python3/dist-packages/nipype/utils/subprocess.py:34: DeprecationWarning: 'locale.getdefaultlocale' is deprecated and slated for removal in Python 3.15. Use setlocale(), getencoding() and getlocale() instead. self.default_encoding = locale.getdefaultlocale()[1] or "UTF-8" heudiconv/tests/test_convert.py::test_b0dwi_for_fmap /usr/lib/python3/dist-packages/pydicom/valuerep.py:443: UserWarning: The value length (22) exceeds the maximum length of 16 allowed for VR SH. warnings.warn(msg) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ FAILED heudiconv/tests/test_heuristics.py::test_reproin_largely_smoke[invocation0-reproin] ==== 1 failed, 104 passed, 10 skipped, 1 deselected, 99 warnings in 59.43s ===== E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.12_heudiconv/build; python3.12 -m pytest heudiconv/tests/test_* -k 'not test_bvals_are_zero' I: pybuild pybuild:308: cp -a heudiconv/tests /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/ I: pybuild base:311: cd /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build; python3.11 -m pytest heudiconv/tests/test_* -k 'not test_bvals_are_zero' ============================= test session starts ============================== platform linux -- Python 3.11.9, pytest-8.1.2, pluggy-1.5.0 rootdir: /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build configfile: pyproject.toml collected 116 items / 1 deselected / 115 selected heudiconv/tests/test_archives.py .......... [ 8%] heudiconv/tests/test_bids.py ..................................s. [ 40%] heudiconv/tests/test_convert.py .......... [ 48%] heudiconv/tests/test_dicoms.py .........ss [ 58%] heudiconv/tests/test_heuristics.py .F......... [ 67%] heudiconv/tests/test_main.py .............. [ 80%] heudiconv/tests/test_monitor.py ssss [ 83%] heudiconv/tests/test_queue.py ... [ 86%] heudiconv/tests/test_regression.py sss. [ 89%] heudiconv/tests/test_tarballs.py . [ 90%] heudiconv/tests/test_utils.py ........... [100%] =================================== FAILURES =================================== _______________ test_reproin_largely_smoke[invocation0-reproin] ________________ tmp_path = PosixPath('/tmp/pytest-of-pbuilder1/pytest-1/test_reproin_largely_smoke_inv0') heuristic = 'reproin' invocation = ['--files', '/build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests/data'] @pytest.mark.parametrize("heuristic", ["reproin", "convertall"]) @pytest.mark.parametrize( "invocation", [ ["--files", TESTS_DATA_PATH], # our new way with automated grouping ["-d", f"{TESTS_DATA_PATH}/{{subject}}/*", "-s", "01-fmap_acq-3mm"], # "old" way specifying subject # should produce the same results ], ) @pytest.mark.skipif(Dataset is None, reason="no datalad") def test_reproin_largely_smoke(tmp_path: Path, heuristic: str, invocation: str) -> None: is_bids = True if heuristic == "reproin" else False args = [ "--random-seed", "1", "-f", heuristic, "-c", "dcm2niix", "-o", str(tmp_path), ] if is_bids: args.append("-b") args.append("--datalad") args.extend(invocation) # Test some safeguards if invocation[0] == "--files": # Multiple subjects must not be specified -- only a single one could # be overridden from the command line with pytest.raises(ValueError): runner(args + ["--subjects", "sub1", "sub2"]) if heuristic != "reproin": # if subject is not overridden, raise error with pytest.raises(NotImplementedError): runner(args) return runner(args) ds = Dataset(tmp_path) assert ds.is_installed() assert not ds.repo.dirty head = ds.repo.get_hexsha() # and if we rerun -- should fail lgr.info( "RERUNNING, expecting to FAIL since the same everything " "and -c specified so we did conversion already" ) with pytest.raises(RuntimeError): runner(args) # but there should be nothing new assert not ds.repo.dirty # TODO: remove whenever https://github.com/datalad/datalad/issues/6843 # is fixed/released buggy_datalad = (ds.pathobj / ".gitmodules").read_text().splitlines().count( '[submodule "Halchenko"]' ) > 1 assert head == ds.repo.get_hexsha() or buggy_datalad # unless we pass 'overwrite' flag > runner(args + ["--overwrite"]) heudiconv/tests/test_heuristics.py:120: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ heudiconv/cli/run.py:30: in main workflow(**kwargs) heudiconv/main.py:410: in workflow study_sessions = get_study_sessions( heudiconv/parser.py:221: in get_study_sessions seqinfo_dict = group_dicoms_into_seqinfos( heudiconv/dicoms.py:324: in group_dicoms_into_seqinfos mwinfo = validate_dicom(filename, dcmfilter) heudiconv/dicoms.py:157: in validate_dicom mw = dw.wrapper_from_file(fl, force=True, stop_before_pixels=True) /usr/lib/python3/dist-packages/nibabel/nicom/dicomwrappers.py:58: in wrapper_from_file dcm_data = pydicom.dcmread(fobj, *args, **kwargs) /usr/lib/python3/dist-packages/pydicom/filereader.py:1030: in dcmread dataset = read_partial( /usr/lib/python3/dist-packages/pydicom/filereader.py:852: in read_partial dataset = read_dataset( /usr/lib/python3/dist-packages/pydicom/filereader.py:427: in read_dataset raw_data_element = next(de_gen) /usr/lib/python3/dist-packages/pydicom/filereader.py:207: in data_element_generator fp_read(length) if length > 0 _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = , size = 1768444706 def read(self, size: int = -1, /) -> bytes: > return self.fobj.read(size) E MemoryError /usr/lib/python3/dist-packages/nibabel/openers.py:223: MemoryError ----------------------------- Captured stdout call ----------------------------- create(ok): /tmp/pytest-of-pbuilder1/pytest-1/test_reproin_largely_smoke_inv0 (dataset) add(ok): head (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): head (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): advanced applications libraries (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): advanced applications libraries (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): .gitattributes (file) save(ok): . (dataset) action summary: add (ok: 1) save (ok: 1) add(ok): advanced applications libraries (dataset) add(ok): .gitmodules (file) save(ok): head (dataset) add(ok): head (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) action summary: add (ok: 4) save (notneeded: 1, ok: 2) add(ok): .heudiconv (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): .heudiconv (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): dbictest1/info/dbictest1.auto.txt (file) add(ok): dbictest1/info/dbictest1.edit.txt (file) add(ok): dbictest1/info/dicominfo.tsv (file) add(ok): dbictest1/info/filegroup.json (file) add(ok): dbictest1/info/heuristic.py (file) save(ok): .heudiconv (dataset) add(ok): .heudiconv (dataset) add(ok): .gitmodules (file) add(ok): .bidsignore (file) add(ok): .gitignore (file) add(ok): CHANGES (file) add(ok): README (file) add(ok): dataset_description.json (file) add(ok): participants.json (file) add(ok): participants.tsv (file) add(ok): scans.json (file) add(ok): sourcedata/README (file) add(ok): sourcedata/sub-dbictest1/anat/sub-dbictest1_scout.dicom.tgz (file) save(ok): . (dataset) action summary: add (ok: 17) save (ok: 2) add(ok): advanced applications libraries (dataset) add(ok): .gitmodules (file) save(ok): head (dataset) add(ok): head (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) action summary: add (ok: 4) save (notneeded: 2, ok: 2) add(ok): Development (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): Development (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): Functional (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): Functional (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): .gitattributes (file) save(ok): . (dataset) action summary: add (ok: 1) save (ok: 1) add(ok): Functional (dataset) add(ok): .gitmodules (file) save(ok): Development (dataset) add(ok): Development (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) action summary: add (ok: 4) save (notneeded: 1, ok: 2) add(ok): .heudiconv (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): .heudiconv (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): o6jgilro/info/dicominfo.tsv (file) add(ok): o6jgilro/info/filegroup.json (file) add(ok): o6jgilro/info/heuristic.py (file) add(ok): o6jgilro/info/o6jgilro.auto.txt (file) add(ok): o6jgilro/info/o6jgilro.edit.txt (file) save(ok): .heudiconv (dataset) add(ok): .heudiconv (dataset) add(ok): .gitmodules (file) add(ok): .bidsignore (file) add(ok): .gitignore (file) add(ok): CHANGES (file) add(ok): README (file) add(ok): dataset_description.json (file) add(ok): participants.json (file) add(ok): participants.tsv (file) add(ok): scans.json (file) add(ok): sourcedata/README (file) add(ok): sourcedata/sub-o6jgilro/anat/sub-o6jgilro_32ch-head-coil_scout.dicom.tgz (file) save(ok): . (dataset) action summary: add (ok: 17) save (ok: 2) add(ok): Functional (dataset) add(ok): .gitmodules (file) save(ok): Development (dataset) add(ok): Development (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) action summary: add (ok: 4) save (notneeded: 2, ok: 2) add(ok): Halchenko (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): Halchenko (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): Yarik (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): Yarik (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): 950_bids_test4 (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): 950_bids_test4 (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): .gitattributes (file) save(ok): . (dataset) action summary: add (ok: 1) save (ok: 1) add(ok): 950_bids_test4 (dataset) add(ok): .gitmodules (file) save(ok): Halchenko/Yarik (dataset) add(ok): Yarik (dataset) add(ok): .gitmodules (file) save(ok): Halchenko (dataset) add(ok): Halchenko (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) action summary: add (ok: 6) save (notneeded: 1, ok: 3) 240512-10:35:16,789 nipype.workflow INFO: [Node] Setting-up "convert" in "/tmp/dcm2niix8_3t7_k4/convert". 240512-10:35:16,793 nipype.workflow INFO: [Node] Executing "convert" 240512-10:35:16,822 nipype.interface INFO: stdout 2024-05-12T10:35:16.822442:Chris Rorden's dcm2niiX version v1.0.20220720 (JP2:OpenJPEG) GCC13.2.0 (32-bit Linux) 240512-10:35:16,822 nipype.interface INFO: stdout 2024-05-12T10:35:16.822442:Found 1 DICOM file(s) 240512-10:35:16,822 nipype.interface INFO: stdout 2024-05-12T10:35:16.822442:Convert 1 DICOM as /tmp/pytest-of-pbuilder1/pytest-1/test_reproin_largely_smoke_inv0/Halchenko/Yarik/950_bids_test4/sub-phantom1sid1/ses-localizer/fmap/sub-phantom1sid1_ses-localizer_acq-3mm_phasediff_heudiconv137_e2_ph (64x64x1x1) 240512-10:35:16,823 nipype.interface INFO: stdout 2024-05-12T10:35:16.823309:Conversion required 0.008609 seconds (0.008224 for core code). 240512-10:35:16,882 nipype.workflow INFO: [Node] Finished "convert", elapsed time 0.087742s. 240512-10:35:16,912 nipype.workflow INFO: [Node] Setting-up "embedder" in "/tmp/embedmeta5rr66xp7/embedder". 240512-10:35:16,918 nipype.workflow INFO: [Node] Executing "embedder" 240512-10:35:16,977 nipype.workflow INFO: [Node] Finished "embedder", elapsed time 0.057683s. add(ok): .heudiconv (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): .heudiconv (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): phantom1sid1/ses-localizer/info/dicominfo_ses-localizer.tsv (file) add(ok): phantom1sid1/ses-localizer/info/filegroup_ses-localizer.json (file) add(ok): phantom1sid1/ses-localizer/info/heuristic.py (file) add(ok): phantom1sid1/ses-localizer/info/phantom1sid1_ses-localizer.auto.txt (file) add(ok): phantom1sid1/ses-localizer/info/phantom1sid1_ses-localizer.edit.txt (file) save(ok): .heudiconv (dataset) add(ok): .heudiconv (dataset) add(ok): .gitmodules (file) add(ok): .bidsignore (file) add(ok): .gitignore (file) add(ok): CHANGES (file) add(ok): README (file) add(ok): dataset_description.json (file) add(ok): participants.json (file) add(ok): participants.tsv (file) add(ok): scans.json (file) add(ok): sourcedata/README (file) add(ok): sourcedata/sub-phantom1sid1/ses-localizer/anat/sub-phantom1sid1_ses-localizer_scout.dicom.tgz (file) add(ok): sourcedata/sub-phantom1sid1/ses-localizer/fmap/sub-phantom1sid1_ses-localizer_acq-3mm_phasediff.dicom.tgz (file) add(ok): sub-phantom1sid1/ses-localizer/fmap/sub-phantom1sid1_ses-localizer_acq-3mm_phasediff.json (file) add(ok): sub-phantom1sid1/ses-localizer/fmap/sub-phantom1sid1_ses-localizer_acq-3mm_phasediff.nii.gz (file) add(ok): sub-phantom1sid1/ses-localizer/sub-phantom1sid1_ses-localizer_scans.tsv (file) save(ok): . (dataset) action summary: add (ok: 21) save (ok: 2) add(ok): 950_bids_test4 (dataset) add(ok): .gitmodules (file) save(ok): Halchenko/Yarik (dataset) add(ok): Yarik (dataset) add(ok): .gitmodules (file) save(ok): Halchenko (dataset) add(ok): Halchenko (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) action summary: add (ok: 6) save (notneeded: 2, ok: 3) add(ok): Chen (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): Chen (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): Matthews (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): Matthews (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): 102TD_Development (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): 102TD_Development (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): .gitattributes (file) save(ok): . (dataset) action summary: add (ok: 1) save (ok: 1) add(ok): 102TD_Development (dataset) add(ok): .gitmodules (file) save(ok): Chen/Matthews (dataset) add(ok): Matthews (dataset) add(ok): .gitmodules (file) save(ok): Chen (dataset) add(ok): Chen (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) action summary: add (ok: 6) save (notneeded: 1, ok: 3) add(ok): .heudiconv (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): .heudiconv (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): phasmr6335/info/dicominfo.tsv (file) add(ok): phasmr6335/info/filegroup.json (file) add(ok): phasmr6335/info/heuristic.py (file) add(ok): phasmr6335/info/phasmr6335.auto.txt (file) add(ok): phasmr6335/info/phasmr6335.edit.txt (file) save(ok): .heudiconv (dataset) add(ok): .heudiconv (dataset) add(ok): .gitmodules (file) add(ok): .bidsignore (file) add(ok): .gitignore (file) add(ok): CHANGES (file) add(ok): README (file) add(ok): dataset_description.json (file) add(ok): participants.json (file) add(ok): participants.tsv (file) add(ok): scans.json (file) add(ok): sourcedata/README (file) add(ok): sourcedata/sub-phasmr6335/anat/sub-phasmr6335_scout.dicom.tgz (file) save(ok): . (dataset) action summary: add (ok: 17) save (ok: 2) add(ok): 102TD_Development (dataset) add(ok): .gitmodules (file) save(ok): Chen/Matthews (dataset) add(ok): Matthews (dataset) add(ok): .gitmodules (file) save(ok): Chen (dataset) add(ok): Chen (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) action summary: add (ok: 6) save (notneeded: 2, ok: 3) add(ok): Research (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): Research (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): MCBI_TESTING (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): MCBI_TESTING (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): .gitattributes (file) save(ok): . (dataset) action summary: add (ok: 1) save (ok: 1) add(ok): MCBI_TESTING (dataset) add(ok): .gitmodules (file) save(ok): Research (dataset) add(ok): Research (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) action summary: add (ok: 4) save (notneeded: 1, ok: 2) add(ok): .heudiconv (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): .heudiconv (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): crlab/info/crlab.auto.txt (file) add(ok): crlab/info/crlab.edit.txt (file) add(ok): crlab/info/dicominfo.tsv (file) add(ok): crlab/info/filegroup.json (file) add(ok): crlab/info/heuristic.py (file) save(ok): .heudiconv (dataset) add(ok): .heudiconv (dataset) add(ok): .gitmodules (file) add(ok): .bidsignore (file) add(ok): .gitignore (file) add(ok): CHANGES (file) add(ok): README (file) add(ok): dataset_description.json (file) add(ok): participants.json (file) add(ok): participants.tsv (file) add(ok): scans.json (file) save(ok): . (dataset) action summary: add (ok: 15) save (ok: 2) add(ok): MCBI_TESTING (dataset) add(ok): .gitmodules (file) save(ok): Research (dataset) add(ok): Research (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) action summary: add (ok: 4) save (notneeded: 2, ok: 2) add(ok): Investigators (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): Investigators (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): Winawer (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): Winawer (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): .gitattributes (file) save(ok): . (dataset) action summary: add (ok: 1) save (ok: 1) add(ok): Winawer (dataset) add(ok): .gitmodules (file) save(ok): Investigators (dataset) add(ok): Investigators (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) action summary: add (ok: 4) save (notneeded: 1, ok: 2) add(ok): .heudiconv (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) create(ok): .heudiconv (dataset) action summary: add (ok: 2) create (ok: 1) save (ok: 1) add(ok): ke6hl9lm/info/dicominfo.tsv (file) add(ok): ke6hl9lm/info/filegroup.json (file) add(ok): ke6hl9lm/info/heuristic.py (file) add(ok): ke6hl9lm/info/ke6hl9lm.auto.txt (file) add(ok): ke6hl9lm/info/ke6hl9lm.edit.txt (file) save(ok): .heudiconv (dataset) add(ok): .heudiconv (dataset) add(ok): .gitmodules (file) add(ok): .bidsignore (file) add(ok): .gitignore (file) add(ok): CHANGES (file) add(ok): README (file) add(ok): dataset_description.json (file) add(ok): participants.json (file) add(ok): participants.tsv (file) add(ok): scans.json (file) save(ok): . (dataset) action summary: add (ok: 15) save (ok: 2) add(ok): Winawer (dataset) add(ok): .gitmodules (file) save(ok): Investigators (dataset) add(ok): Investigators (dataset) add(ok): .gitmodules (file) save(ok): . (dataset) action summary: add (ok: 4) save (notneeded: 2, ok: 2) action summary: save (notneeded: 2) add(ok): head (dataset) add(ok): .gitmodules (file) action summary: add (ok: 2) save (notneeded: 4) action summary: save (notneeded: 2) add(ok): Development (dataset) add(ok): .gitmodules (file) action summary: add (ok: 2) save (notneeded: 4) ------------------------------ Captured log call ------------------------------- WARNING heudiconv.main:main.py:362 Could not check for version updates: Connection to server could not be made WARNING heudiconv.dicoms:dicoms.py:176 Ignoring /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests/data/sample_nifti.json since not quite a "normal" DICOM: 'FileDataset' object has no attribute 'SeriesNumber' WARNING heudiconv.dicoms:dicoms.py:176 Ignoring /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests/data/sample_nifti.nii.gz since not quite a "normal" DICOM: 'FileDataset' object has no attribute 'SeriesNumber' WARNING heudiconv.dicoms:dicoms.py:176 Ignoring /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build/heudiconv/tests/data/sample_nifti_params.txt since not quite a "normal" DICOM: 'FileDataset' object has no attribute 'SeriesNumber' INFO datalad:log.py:432 Clear progress bars INFO datalad:log.py:432 Refresh progress bars INFO datalad.core.local.save:log.py:432 Total: starting INFO datalad.core.local.save:log.py:432 INFO datalad:log.py:432 Clear progress bars INFO datalad:log.py:432 Refresh progress bars INFO datalad:log.py:432 Clear progress bars INFO datalad:log.py:432 Refresh progress bars INFO datalad.core.local.save:log.py:432 Total: processed result for /tmp/pytest-of-pbuilder1/pytest-1/test_reproin_largely_smoke_inv0 INFO datalad:log.py:432 Clear progress bars INFO datalad:log.py:432 Refresh progress bars INFO datalad.core.local.save:log.py:432 Total: done INFO datalad:log.py:432 Clear progress bars 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protocol_name, series_description fields WARNING heudiconv:reproin.py:662 Could not figure out where to stick 1 sequences: ['99-Phoenix Document'] WARNING heudiconv.bids:bids.py:1025 We cannot add the IntendedFor field: no fmap/ in /tmp/pytest-of-pbuilder1/pytest-1/test_reproin_largely_smoke_inv0/Development/Functional/sub-o6jgilro INFO datalad.core.local.save:log.py:432 Total: starting INFO datalad.core.local.save:log.py:432 INFO datalad.core.local.save:log.py:432 Total: processed result for /tmp/pytest-of-pbuilder1/pytest-1/test_reproin_largely_smoke_inv0/Development/Functional INFO datalad.core.local.save:log.py:432 Total: done INFO datalad.core.local.save:log.py:432 Total: starting INFO datalad.core.local.save:log.py:432 INFO datalad:log.py:432 Clear progress bars INFO datalad:log.py:432 Refresh progress bars INFO datalad:log.py:432 Clear progress bars INFO datalad:log.py:432 Refresh progress bars INFO datalad.core.local.save:log.py:432 Total: processed result for 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Setting-up "convert" in "/tmp/dcm2niix8_3t7_k4/convert". INFO nipype.workflow:nodes.py:716 [Node] Executing "convert" INFO nipype.interface:subprocess.py:69 stdout 2024-05-12T10:35:16.822442:Chris Rorden's dcm2niiX version v1.0.20220720 (JP2:OpenJPEG) GCC13.2.0 (32-bit Linux) INFO nipype.interface:subprocess.py:69 stdout 2024-05-12T10:35:16.822442:Found 1 DICOM file(s) INFO nipype.interface:subprocess.py:69 stdout 2024-05-12T10:35:16.822442:Convert 1 DICOM as /tmp/pytest-of-pbuilder1/pytest-1/test_reproin_largely_smoke_inv0/Halchenko/Yarik/950_bids_test4/sub-phantom1sid1/ses-localizer/fmap/sub-phantom1sid1_ses-localizer_acq-3mm_phasediff_heudiconv137_e2_ph (64x64x1x1) INFO nipype.interface:subprocess.py:69 stdout 2024-05-12T10:35:16.823309:Conversion required 0.008609 seconds (0.008224 for core code). INFO nipype.workflow:nodes.py:723 [Node] Finished "convert", elapsed time 0.087742s. INFO nipype.workflow:nodes.py:453 [Node] Setting-up "embedder" in "/tmp/embedmeta5rr66xp7/embedder". INFO nipype.workflow:nodes.py:716 [Node] Executing "embedder" INFO nipype.workflow:nodes.py:723 [Node] Finished "embedder", elapsed time 0.057683s. 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Total: processed result for /tmp/pytest-of-pbuilder1/pytest-1/test_reproin_largely_smoke_inv0/Development/Functional/.heudiconv INFO datalad.core.local.save:log.py:432 Total: processed result for /tmp/pytest-of-pbuilder1/pytest-1/test_reproin_largely_smoke_inv0/Development/Functional INFO datalad.core.local.save:log.py:432 Total: processed result for /tmp/pytest-of-pbuilder1/pytest-1/test_reproin_largely_smoke_inv0/Development INFO datalad:log.py:432 Clear progress bars INFO datalad:log.py:432 Refresh progress bars INFO datalad:log.py:432 Clear progress bars INFO datalad:log.py:432 Refresh progress bars INFO datalad.core.local.save:log.py:432 Total: processed result for /tmp/pytest-of-pbuilder1/pytest-1/test_reproin_largely_smoke_inv0 INFO datalad.core.local.save:log.py:432 Total: done INFO datalad:log.py:432 Clear progress bars INFO datalad:log.py:432 Refresh progress bars WARNING heudiconv.main:main.py:362 Could not check for version updates: Connection to server could not be made =============================== warnings summary =============================== ../../../../../../usr/lib/python3/dist-packages/traits/observation/_generated_parser.py:258 /usr/lib/python3/dist-packages/traits/observation/_generated_parser.py:258: DeprecationWarning: module 'sre_parse' is deprecated import sre_parse ../../../../../../usr/lib/python3/dist-packages/traits/observation/_generated_parser.py:259 /usr/lib/python3/dist-packages/traits/observation/_generated_parser.py:259: DeprecationWarning: module 'sre_constants' is deprecated import sre_constants heudiconv/tests/test_convert.py::test_b0dwi_for_fmap heudiconv/tests/test_convert.py::test_b0dwi_for_fmap /usr/lib/python3/dist-packages/nipype/utils/filemanip.py:696: DeprecationWarning: 'locale.getdefaultlocale' is deprecated and slated for removal in Python 3.15. Use setlocale(), getencoding() and getlocale() instead. default_encoding = encoding or locale.getdefaultlocale()[1] or "UTF-8" heudiconv/tests/test_convert.py: 4 warnings heudiconv/tests/test_dicoms.py: 2 warnings heudiconv/tests/test_heuristics.py: 20 warnings heudiconv/tests/test_main.py: 2 warnings heudiconv/tests/test_regression.py: 4 warnings /usr/lib/python3/dist-packages/nipype/utils/subprocess.py:34: DeprecationWarning: 'locale.getdefaultlocale' is deprecated and slated for removal in Python 3.15. Use setlocale(), getencoding() and getlocale() instead. self.default_encoding = locale.getdefaultlocale()[1] or "UTF-8" heudiconv/tests/test_convert.py::test_b0dwi_for_fmap /usr/lib/python3/dist-packages/pydicom/valuerep.py:443: UserWarning: The value length (22) exceeds the maximum length of 16 allowed for VR SH. warnings.warn(msg) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ FAILED heudiconv/tests/test_heuristics.py::test_reproin_largely_smoke[invocation0-reproin] ==== 1 failed, 104 passed, 10 skipped, 1 deselected, 37 warnings in 56.27s ===== E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd /build/reproducible-path/heudiconv-1.1.1/.pybuild/cpython3_3.11_heudiconv/build; python3.11 -m pytest heudiconv/tests/test_* -k 'not test_bvals_are_zero' rm -fr -- /tmp/dh-xdg-rundir-TuedW96E dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.12 3.11" returned exit code 13 make: *** [debian/rules:19: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/7723 and its subdirectories Sun May 12 22:35:58 UTC 2024 W: No second build log, what happened?