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This page was generated on 2024-05-04 11:41:06 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1941/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SeqArray 1.44.0  (landing page)
Xiuwen Zheng
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/SeqArray
git_branch: RELEASE_3_19
git_last_commit: 9408216
git_last_commit_date: 2024-04-30 10:31:00 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for SeqArray on kunpeng2


To the developers/maintainers of the SeqArray package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SeqArray.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: SeqArray
Version: 1.44.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:SeqArray.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings SeqArray_1.44.0.tar.gz
StartedAt: 2024-05-04 11:55:11 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 11:59:25 -0000 (Sat, 04 May 2024)
EllapsedTime: 254.4 seconds
RetCode: 0
Status:   OK  
CheckDir: SeqArray.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:SeqArray.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings SeqArray_1.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SeqArray.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SeqArray/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SeqArray’ version ‘1.44.0’
* 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 ‘SeqArray’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking installed package size ... NOTE
  installed size is  8.2Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      5.9Mb
* 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 code 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... 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 ... NOTE
Note: information on .o files is not available
File ‘SeqArray/libs/SeqArray.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’, ‘R_new_custom_connection’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/SeqArray.Rcheck/00check.log’
for details.


Installation output

SeqArray.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL SeqArray
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘SeqArray’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/gdsfmt/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/gdsfmt/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c ConvToGDS.cpp -o ConvToGDS.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/gdsfmt/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/gdsfmt/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c FileMerge.cpp -o FileMerge.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/gdsfmt/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c GetData.cpp -o GetData.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/gdsfmt/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c Index.cpp -o Index.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/gdsfmt/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c LinkSNPRelate.cpp -o LinkSNPRelate.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/gdsfmt/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c Methods.cpp -o Methods.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/gdsfmt/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c R_SeqArray.c -o R_SeqArray.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/gdsfmt/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c ReadBySample.cpp -o ReadBySample.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/gdsfmt/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c ReadByUnit.cpp -o ReadByUnit.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/gdsfmt/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c ReadByVariant.cpp -o ReadByVariant.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/gdsfmt/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c SeqArray.cpp -o SeqArray.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/gdsfmt/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c pkg_test.cpp -o pkg_test.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/gdsfmt/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c samtools_ext.c -o samtools_ext.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/gdsfmt/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c vectorization.cpp -o vectorization.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o SeqArray.so ConvGDS2VCF.o ConvToGDS.o ConvVCF2GDS.o FileMerge.o GetData.o Index.o LinkSNPRelate.o Methods.o R_SeqArray.o ReadBySample.o ReadByUnit.o ReadByVariant.o SeqArray.o pkg_test.o samtools_ext.o vectorization.o -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-SeqArray/00new/SeqArray/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SeqArray)

Tests output

SeqArray.Rcheck/tests/test.Rout


R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> if (.Platform$OS.type != "windows")
+     BiocGenerics:::testPackage("SeqArray")
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following object is masked from 'package:SeqArray':

    rowRanges


Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

The following object is masked from 'package:SeqArray':

    rowRanges

Loading required package: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
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")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians


Attaching package: 'SummarizedExperiment'

The following object is masked from 'package:SeqArray':

    colData

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit


Attaching package: 'VariantAnnotation'

The following objects are masked from 'package:SeqArray':

    alt, filt, fixed, geno, header, info, qual, ref

The following object is masked from 'package:base':

    tabulate

[W::bcf_hdr_check_sanity] GL should be declared as Number=G
# of selected variants: 898

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 8s

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 8s

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 10s

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 4s
# of selected variants: 655

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 4s

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 4s

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 6s

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 3s

Attaching package: 'Matrix'

The following object is masked from 'package:VariantAnnotation':

    expand

The following object is masked from 'package:S4Vectors':

    expand

# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348


RUNIT TEST PROTOCOL -- Sat May  4 11:59:20 2024 
*********************************************** 
Number of test functions: 28 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
SeqArray RUnit Tests - 28 test functions, 0 errors, 0 failures
Number of test functions: 28 
Number of errors: 0 
Number of failures: 0 
There were 50 or more warnings (use warnings() to see the first 50)
> 
> proc.time()
   user  system elapsed 
 62.339  65.886 110.420 

Example timings

SeqArray.Rcheck/SeqArray-Ex.timings

nameusersystemelapsed
SeqArray-package0.4750.0360.514
SeqVarGDSClass-class0.1550.0000.155
seqAddValue0.1520.0080.160
seqAlleleFreq0.0640.0000.065
seqApply0.1490.0000.148
seqAsVCF0.0030.0000.002
seqBED2GDS0.2950.0240.322
seqBlockApply0.0730.0000.073
seqCheck0.0270.0040.031
seqDelete0.1140.0050.119
seqDigest0.0210.0020.024
seqEmptyFile0.0220.0000.022
seqExampleFileName0.0030.0000.003
seqExport0.5110.0840.597
seqGDS2SNP0.0540.0080.062
seqGDS2VCF0.6300.0160.650
seqGet2bGeno0.0120.0000.012
seqGetData1.7440.0121.760
seqGetFilter0.0670.0030.070
seqMerge0.7960.0750.876
seqMissing0.0830.0000.083
seqNewVarData0.0000.0030.003
seqNumAllele0.0040.0000.003
seqOpen0.0620.0040.066
seqOptimize0.1740.0160.193
seqParallel0.1400.4130.280
seqParallelSetup0.0880.0820.121
seqRecompress0.2550.3140.520
seqResetVariantID0.0210.0120.034
seqSNP2GDS1.3660.0361.407
seqSetFilter0.0820.0190.102
seqSetFilterCond0.0600.0240.084
seqStorageOption0.6450.0600.713
seqSummary0.1460.0110.161
seqSystem0.0010.0000.000
seqTranspose0.2150.0200.236
seqUnitApply0.3230.1290.333
seqUnitFilterCond0.0750.0080.083
seqUnitSlidingWindows0.050.000.05
seqUnitSubset0.0700.0040.074
seqVCF2GDS0.5660.2960.705
seqVCF_Header0.0900.0190.110
seqVCF_SampID0.0010.0010.002