Back to Multiple platform build/check report for BioC 3.16:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2023-04-12 11:05:19 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

CHECK results for SeqArray on nebbiolo2


To the developers/maintainers of the SeqArray package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1840/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SeqArray 1.38.0  (landing page)
Xiuwen Zheng
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/SeqArray
git_branch: RELEASE_3_16
git_last_commit: 37a86c1
git_last_commit_date: 2022-11-01 11:08:00 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: SeqArray
Version: 1.38.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:SeqArray.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings SeqArray_1.38.0.tar.gz
StartedAt: 2023-04-10 23:56:37 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-11 00:01:39 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 301.4 seconds
RetCode: 0
Status:   OK  
CheckDir: SeqArray.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:SeqArray.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings SeqArray_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/SeqArray.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘SeqArray/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SeqArray’ version ‘1.38.0’
* 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
* checking installed package size ... NOTE
  installed size is  8.1Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      5.8Mb
* 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 ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘OverviewSlides.Rmd’... OK
  ‘SeqArray.Rmd’ using ‘UTF-8’... OK
  ‘SeqArrayTutorial.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/SeqArray.Rcheck/00check.log’
for details.



Installation output

SeqArray.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL SeqArray
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘SeqArray’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/gdsfmt/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/gdsfmt/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ConvToGDS.cpp -o ConvToGDS.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/gdsfmt/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/gdsfmt/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c FileMerge.cpp -o FileMerge.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/gdsfmt/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c GetData.cpp -o GetData.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/gdsfmt/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c Index.cpp -o Index.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/gdsfmt/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c LinkSNPRelate.cpp -o LinkSNPRelate.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/gdsfmt/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c Methods.cpp -o Methods.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/gdsfmt/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c R_SeqArray.c -o R_SeqArray.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/gdsfmt/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ReadBySample.cpp -o ReadBySample.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/gdsfmt/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ReadByUnit.cpp -o ReadByUnit.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/gdsfmt/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ReadByVariant.cpp -o ReadByVariant.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/gdsfmt/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c SeqArray.cpp -o SeqArray.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/gdsfmt/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pkg_test.cpp -o pkg_test.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/gdsfmt/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c samtools_ext.c -o samtools_ext.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/gdsfmt/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c vectorization.c -o vectorization.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.16-bioc/R/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/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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, sort, 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 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, 7s

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 5s

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 1s
# of selected variants: 655

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

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

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

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 1s

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 -- Mon Apr 10 23:59:53 2023 
*********************************************** 
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 
 58.288  59.846  90.639 

Example timings

SeqArray.Rcheck/SeqArray-Ex.timings

nameusersystemelapsed
SeqArray-package0.3530.0120.367
SeqVarGDSClass-class0.1100.0040.114
seqAddValue0.1530.0080.161
seqAlleleFreq0.0590.0000.059
seqApply0.1180.0040.122
seqAsVCF0.0020.0000.002
seqBED2GDS0.2570.0320.290
seqBlockApply0.0480.0040.052
seqCheck0.0210.0040.024
seqDelete0.0790.0020.080
seqDigest0.0190.0020.021
seqEmptyFile0.0170.0000.016
seqExampleFileName0.0020.0000.001
seqExport0.8260.0720.898
seqGDS2SNP0.0670.0040.070
seqGDS2VCF0.5310.0000.531
seqGet2bGeno0.0090.0000.009
seqGetData1.4120.0321.444
seqGetFilter0.0410.0010.041
seqMerge0.6260.0990.725
seqMissing0.0560.0040.060
seqNewVarData0.0020.0000.002
seqNumAllele0.0010.0020.003
seqOpen0.0360.0050.042
seqOptimize0.1590.0080.167
seqParallel0.1380.3350.250
seqParallelSetup0.0550.0840.106
seqRecompress0.3280.0820.347
seqResetVariantID0.0210.0040.026
seqSNP2GDS2.0420.0842.127
seqSetFilter0.0540.0000.055
seqSetFilterCond0.0420.0000.042
seqStorageOption0.4670.0240.491
seqSummary0.1010.0080.109
seqSystem000
seqTranspose0.1780.0120.190
seqUnitApply0.1960.1390.235
seqUnitFilterCond0.0560.0040.061
seqUnitSlidingWindows0.0350.0000.035
seqUnitSubset0.0450.0080.053
seqVCF2GDS0.5190.2880.643
seqVCF_Header0.1020.0000.102
seqVCF_SampID0.0020.0000.001