Attachment 1444763 Details for Bug 1555529 – build.log

build.log

build.log (text/plain), 11.78 KB, created by Fedora Release Engineering on 2018-05-28 22:32:24 UTC

(hide)

Description:

Filename:

MIME Type:

Creator: Fedora Release Engineering

Created: 2018-05-28 22:32:24 UTC

Size: 11.78 KB

patch

obsolete

>Mock Version: 1.3.4
>Mock Version: 1.3.4
>ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target noarch --nodeps /builddir/build/SPECS/R-affydata.spec'], chrootPath='/var/lib/mock/f29-build-12561431-918708/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0xffffa3a97f98>timeout=172800uid=1000gid=425user='mockbuild'nspawn_args=[]printOutput=False)
>Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target noarch --nodeps /builddir/build/SPECS/R-affydata.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False
>Building target platforms: noarch
>Building for target noarch
>Wrote: /builddir/build/SRPMS/R-affydata-1.16.0-5.fc29.src.rpm
>Child return code was: 0
>ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target noarch --nodeps /builddir/build/SPECS/R-affydata.spec'], chrootPath='/var/lib/mock/f29-build-12561431-918708/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0xffffa3a97f98>timeout=172800uid=1000gid=425user='mockbuild'nspawn_args=[]printOutput=False)
>Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target noarch --nodeps /builddir/build/SPECS/R-affydata.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False
>Building target platforms: noarch
>Building for target noarch
>Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.ZmFJT7
>+ umask 022
>+ cd /builddir/build/BUILD
>+ cd /builddir/build/BUILD
>+ rm -rf affydata
>+ /usr/bin/mkdir -p affydata
>+ cd affydata
>+ /usr/bin/gzip -dc /builddir/build/SOURCES/affydata_1.16.0.tar.gz
>+ /usr/bin/tar -xof -
>+ STATUS=0
>+ '[' 0 -ne 0 ']'
>+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
>+ exit 0
>Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.hFNDEm
>+ umask 022
>+ cd /builddir/build/BUILD
>+ cd affydata
>+ exit 0
>Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.9nOzrE
>+ umask 022
>+ cd /builddir/build/BUILD
>+ '[' /builddir/build/BUILDROOT/R-affydata-1.16.0-5.fc29.noarch '!=' / ']'
>+ rm -rf /builddir/build/BUILDROOT/R-affydata-1.16.0-5.fc29.noarch
>++ dirname /builddir/build/BUILDROOT/R-affydata-1.16.0-5.fc29.noarch
>+ mkdir -p /builddir/build/BUILDROOT
>+ mkdir /builddir/build/BUILDROOT/R-affydata-1.16.0-5.fc29.noarch
>+ cd affydata
>+ rm -rf /builddir/build/BUILDROOT/R-affydata-1.16.0-5.fc29.noarch
>+ mkdir -p /builddir/build/BUILDROOT/R-affydata-1.16.0-5.fc29.noarch/usr/share/R/library
>+ /usr/bin/R CMD INSTALL affydata -l /builddir/build/BUILDROOT/R-affydata-1.16.0-5.fc29.noarch/usr/share/R/library
>* installing *source* package 'affydata' ...
>** R
>** data
>** inst
>** byte-compile and prepare package for lazy loading
>** help
>*** installing help indices
>  converting help for package 'affydata'
>    finding HTML links ... done
>    Dilution                                html  
>** building package indices
>** installing vignettes
>** testing if installed package can be loaded
>     Package   
>[1,] "affydata"
>     LibPath                                                                        
>[1,] "/builddir/build/BUILDROOT/R-affydata-1.16.0-5.fc29.noarch/usr/share/R/library"
>     Item       Title                        
>[1,] "Dilution" "AffyBatch instance Dilution"
>* DONE (affydata)
>+ test -d affydata/src
>+ rm -rf /builddir/build/BUILDROOT/R-affydata-1.16.0-5.fc29.noarch/usr/share/R/library/R.css
>+ /usr/lib/rpm/find-debuginfo.sh -j4 --strict-build-id -m -i --build-id-seed 1.16.0-5.fc29 --unique-debug-suffix -1.16.0-5.fc29.noarch --unique-debug-src-base R-affydata-1.16.0-5.fc29.noarch --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/affydata
>+ /usr/lib/rpm/check-buildroot
>+ /usr/lib/rpm/redhat/brp-ldconfig
>/sbin/ldconfig: Warning: ignoring configuration file that cannot be opened: /etc/ld.so.conf: No such file or directory
>+ /usr/lib/rpm/brp-compress
>+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
>+ /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1
>+ /usr/lib/rpm/brp-python-hardlink
>+ /usr/lib/rpm/redhat/brp-mangle-shebangs
>Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.XWXnfA
>+ umask 022
>+ cd /builddir/build/BUILD
>+ cd affydata
>+ /usr/bin/R CMD check affydata
>* using log directory '/builddir/build/BUILD/affydata/affydata.Rcheck'
>* using R version 3.5.0 (2018-04-23)
>* using platform: aarch64-redhat-linux-gnu (64-bit)
>* using session charset: ASCII
>* checking for file 'affydata/DESCRIPTION' ... OK
>* this is package 'affydata' version '1.16.0'
>* checking package namespace information ... OK
>* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
>  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
>Warning: unable to access index for repository https://bioconductor.org/packages/3.7/bioc/src/contrib:
>  cannot open URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/PACKAGES'
>Warning: unable to access index for repository https://bioconductor.org/packages/3.7/data/annotation/src/contrib:
>  cannot open URL 'https://bioconductor.org/packages/3.7/data/annotation/src/contrib/PACKAGES'
>Warning: unable to access index for repository https://bioconductor.org/packages/3.7/data/experiment/src/contrib:
>  cannot open URL 'https://bioconductor.org/packages/3.7/data/experiment/src/contrib/PACKAGES'
> OK
>* checking if this is a source package ... OK
>* checking if there is a namespace ... OK
>* checking for executable files ... OK
>* checking for hidden files and directories ... OK
>* checking for portable file names ... OK
>* checking for sufficient/correct file permissions ... OK
>* checking whether package 'affydata' can be installed ... OK
>* checking installed package size ... NOTE
>  installed size is 23.5Mb
>  sub-directories of 1Mb or more:
>    celfiles       16.2Mb
>    data            4.4Mb
>    extracelfiles   2.7Mb
>* checking package directory ... OK
>* checking 'build' directory ... OK
>* checking DESCRIPTION meta-information ... OK
>* checking top-level files ... OK
>* checking for left-over files ... OK
>* checking index information ... OK
>* checking package subdirectories ... OK
>* checking R files for non-ASCII characters ... OK
>* checking R files for syntax errors ... OK
>* checking whether the package can be loaded ... OK
>* checking whether the package can be loaded with stated dependencies ... OK
>* checking whether the package can be unloaded cleanly ... OK
>* checking whether the namespace can be loaded with stated dependencies ... WARNING
>Error: .onLoad failed in loadNamespace() for 'affydata', details:
>  call: data(package = pkgname)
>  error: could not find function "data"
>Execution halted
>A namespace must be able to be loaded with just the base namespace
>loaded: otherwise if the namespace gets loaded by a saved object, the
>session will be unable to start.
>Probably some imports need to be declared in the NAMESPACE file.
>* checking whether the namespace can be unloaded cleanly ... OK
>* checking loading without being on the library search path ... WARNING
>Loading required package: affy
>Error: package 'BiocGenerics' required by 'affy' could not be found
>Execution halted
>It looks like this package has a loading problem when not on .libPaths:
>see the messages for details.
>* checking dependencies in R code ... NOTE
>Package in Depends field not imported from: 'affy'
>  These packages need to be imported from (in the NAMESPACE file)
>  for when this namespace is loaded but not attached.
>* checking S3 generic/method consistency ... OK
>* checking replacement functions ... OK
>* checking foreign function calls ... OK
>* checking R code for possible problems ... NOTE
>Error: .onLoad failed in loadNamespace() for 'affydata', details:
>  call: data(package = pkgname)
>  error: could not find function "data"
>Execution halted
>* checking Rd files ... OK
>* checking Rd metadata ... OK
>* checking Rd cross-references ... OK
>* checking for missing documentation entries ... OK
>* checking for code/documentation mismatches ... OK
>* checking Rd \usage sections ... OK
>* checking Rd contents ... OK
>* checking for unstated dependencies in examples ... OK
>* checking contents of 'data' directory ... OK
>* checking data for non-ASCII characters ... OK
>* checking data for ASCII and uncompressed saves ... WARNING
>  
>  Note: significantly better compression could be obtained
>        by using R CMD build --resave-data
>               old_size new_size compress
>  Dilution.rda    4.4Mb    2.4Mb       xz
>* checking sizes of PDF files under 'inst/doc' ... OK
>* checking installed files from 'inst/doc' ... OK
>* checking files in 'vignettes' ... OK
>* checking examples ... NONE
>* checking for unstated dependencies in vignettes ... NOTE
>'::' or ':::' import not declared from: 'Biobase'
>* checking package vignettes in 'inst/doc' ... OK
>* checking running R code from vignettes ...
>   'affydata.Rnw' ... failed
> ERROR
>Errors in running code in vignettes:
>when running code in 'affydata.Rnw'
>  ...
>Warning: missing cdf environment! in show(AffyBatch)
>AffyBatch object
>size of arrays=640x640 features (38422 kb)
>cdf=HG_U95Av2 (??? affyids)
>number of samples=4
>  When sourcing 'affydata.R':
>Error: package or namespace load failed for 'hgu95av2cdf':
> object 'elementLengths' is not exported by 'namespace:S4Vectors'
>Execution halted
>* checking re-building of vignette outputs ... NOTE
>Error in re-building vignettes:
>  ...
>    IQR, mad, sd, var, xtabs
>The following objects are masked from 'package:base':
>    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
>    as.data.frame, basename, cbind, colMeans, colSums, colnames,
>    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
>    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
>    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
>    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
>    union, unique, unsplit, which, which.max, which.min
>Loading required package: Biobase
>Welcome to Bioconductor
>    Vignettes contain introductory material; view with
>    'browseVignettes()'. To cite Bioconductor, see
>    'citation("Biobase")', and for packages 'citation("pkgname")'.
>Warning: missing cdf environment! in show(AffyBatch)
>Error: processing vignette 'affydata.Rnw' failed with diagnostics:
>package or namespace load failed for 'hgu95av2cdf':
> object 'elementLengths' is not exported by 'namespace:S4Vectors'
>Execution halted
>* checking PDF version of manual ... OK
>* DONE
>Status: 1 ERROR, 3 WARNINGs, 5 NOTEs
>See
>  '/builddir/build/BUILD/affydata/affydata.Rcheck/00check.log'
>for details.
>error: Bad exit status from /var/tmp/rpm-tmp.XWXnfA (%check)
>    Bad exit status from /var/tmp/rpm-tmp.XWXnfA (%check)
>RPM build errors:
>Child return code was: 1
>EXCEPTION: [Error()]
>Traceback (most recent call last):
>  File "/usr/lib/python3.6/site-packages/mockbuild/trace_decorator.py", line 89, in trace
>    result = func(*args, **kw)
>  File "/usr/lib/python3.6/site-packages/mockbuild/util.py", line 582, in do
>    raise exception.Error("Command failed. See logs for output.\n # %s" % (command,), child.returncode)
>mockbuild.exception.Error: Command failed. See logs for output.
> # bash --login -c /usr/bin/rpmbuild -bb --target noarch --nodeps /builddir/build/SPECS/R-affydata.spec

Actions: View

Attachments on bug 1555529: 1444763 | 1444766 | 1444768