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affxparser.check failure #61

Open martin-g opened 1 year ago

martin-g commented 1 year ago 
biocbuild@kunpeng1 ~/git> R CMD build --keep-empty-dirs --no-resave-data affxparser
* checking for file ‘affxparser/DESCRIPTION’ ... OK
* preparing ‘affxparser’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘affxparser_1.71.0.tar.gz’
biocbuild@kunpeng1 ~/git> R CMD check affxparser_1.71.0.tar.gz 
* using log directory ‘/home/biocbuild/git/affxparser.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘affxparser/DESCRIPTION’ ... OK
* this is package ‘affxparser’ version ‘1.71.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘affxparser’ can be installed ... WARNING
Found the following significant warnings:
  fusion/file/CELFileData.cpp:2409:41: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
  fusion/file/CELFileData.cpp:2414:41: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
  fusion/file/CELFileData.cpp:2419:42: warning: taking address of packed member of ‘affxcel::_CELFileTranscriptomeEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
  fusion/file/CELFileData.cpp:2445:37: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
  fusion/file/CELFileData.cpp:2451:37: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
  fusion/file/CELFileData.cpp:2457:38: warning: taking address of packed member of ‘affxcel::_CELFileTranscriptomeEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
  fusion/file/CELFileData.cpp:2506:37: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
  fusion/file/CELFileData.cpp:2509:37: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
  fusion/file/CELFileData.cpp:2512:38: warning: taking address of packed member of ‘affxcel::_CELFileTranscriptomeEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
  fusion/file/CELFileData.cpp:2551:38: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
  fusion/file/CELFileData.cpp:2554:38: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
  fusion/file/CELFileData.cpp:3194:30: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
  fusion/file/CELFileData.cpp:3199:30: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
  fusion/file/CELFileData.cpp:3204:31: warning: taking address of packed member of ‘affxcel::_CELFileTranscriptomeEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
  fusion/file/CELFileData.cpp:3251:31: warning: taking address of packed member of ‘affxcel::_CELFileTranscriptomeEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
  fusion/file/CELFileData.cpp:3255:30: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
  fusion/file/CELFileData.cpp:3294:42: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member]
See ‘/home/biocbuild/git/affxparser.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... NOTE
  installed size is 18.6Mb
  sub-directories of 1Mb or more:
    libs  18.0Mb
* checking package 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 ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) cdfGtypeCelToPQ.Rd:13: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) cdfGtypeCelToPQ.Rd:16: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) readCcg.Rd:62: Escaped LaTeX specials: \#
checkRd: (-1) readCcg.Rd:64: Escaped LaTeX specials: \#
checkRd: (-1) readCcg.Rd:70: Escaped LaTeX specials: \#
checkRd: (-1) readCcg.Rd:72: Escaped LaTeX specials: \#
checkRd: (-1) readCcg.Rd:74: Escaped LaTeX specials: \#
checkRd: (-1) readCcg.Rd:76: Escaped LaTeX specials: \#
* 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 line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
File ‘affxparser/libs/affxparser.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
    Object: ‘fusion/util/Verbose.o’
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
    Objects: ‘fusion/file/TsvFile/TsvFile.o’, ‘fusion/util/Err.o’
  Found ‘abort’, possibly from ‘abort’ (C)
    Objects: ‘fusion/calvin_files/fusion/src/FusionCHPData.o’,
      ‘fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o’,
      ‘fusion/calvin_files/parameter/src/ParameterNameValueType.o’,
      ‘fusion/file/BPMAPFileWriter.o’
  Found ‘exit’, possibly from ‘exit’ (C)
    Objects: ‘fusion/util/Err.o’, ‘R_affx_clf_pgf_parser.o’
  Found ‘printf’, possibly from ‘printf’ (C)
    Object: ‘fusion/file/TsvFile/TsvFile.o’
  Found ‘putchar’, possibly from ‘putchar’ (C)
    Object: ‘fusion/file/TsvFile/TsvFile.o’
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Object: ‘fusion/file/TsvFile/TsvFile.o’
  Found ‘rand’, possibly from ‘rand’ (C)
    Objects: ‘fusion/calvin_files/utils/src/AffymetrixGuid.o’,
      ‘fusion/util/Verbose.o’
  Found ‘sprintf’, possibly from ‘sprintf’ (C)
    Objects: ‘fusion/calvin_files/utils/src/AffymetrixGuid.o’,
      ‘fusion/util/AffxConv.o’, ‘R_affx_cdf_parser.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘fusion/calvin_files/utils/src/AffymetrixGuid.o’
  Found ‘stdout’, possibly from ‘stdout’ (C)
    Object: ‘fusion/util/Util.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘convertCel.R’
  Running ‘readCdfDataFrame.R’
  Running ‘readCdfQc.R’
  Running ‘readCdfUnitsWriteMap.R’
  Running ‘readCdfUnits_etal.R’
  Running ‘readCel.R’
  Running ‘readCelIntensities.R’
  Running ‘readCelRectangle.R’
  Running ‘readCelUnits.R’
  Running ‘readPgf.R’
 ERROR
Running the tests in ‘tests/readPgf.R’ failed.
Last 13 lines of output:
  +     n <- sample(Jall, size=1L)
  +     idxs <- sort(sample(1:Jall, size=n, replace=FALSE))
  +     data <- readPgf(pgf, indices=idxs)
  +     dataS <- subsetPgf(data0, indices=idxs)
  +     for (ff in c("probesetStartAtom", "atomExonPosition"))
  +       data[[ff]] <- dataS[[ff]] <- NULL
  +     stopifnot(all.equal(data, dataS))
  +   }
  + } # if (require("AffymetrixDataTestFiles"))
  Loading required package: AffymetrixDataTestFiles
  Error in readPgfEnv(file, readBody = TRUE, indices = indices) : 
  FATAL ERROR:fusion/file/TsvFile/TsvFile.cpp:953: Conversion error
  TSVERROR: '/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/AffymetrixDataTestFiles/annotationData/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-v1.r4,10_probesets.pgf':90: Conversion of required field 'probeset_id' to int of 'ÿ' failed!
  Calls: readPgf -> as.list -> readPgfEnv
  Execution halted
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/git/affxparser.Rcheck/00check.log’
for details.
martin-g commented 1 year ago

Reported upstream - https://github.com/HenrikBengtsson/affxparser/issues/46