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CHECK report for SeqArray on malbec1

This page was generated on 2020-04-15 12:07:34 -0400 (Wed, 15 Apr 2020).

Package 1559/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SeqArray 1.26.2
Xiuwen Zheng
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/SeqArray
Branch: RELEASE_3_10
Last Commit: e9a1b0d
Last Changed Date: 2019-12-26 16:34:44 -0400 (Thu, 26 Dec 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SeqArray
Version: 1.26.2
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:SeqArray.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings SeqArray_1.26.2.tar.gz
StartedAt: 2020-04-15 01:40:29 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 01:44:34 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 245.5 seconds
RetCode: 0
Status:  OK 
CheckDir: SeqArray.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:SeqArray.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings SeqArray_1.26.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/SeqArray.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SeqArray/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SeqArray’ version ‘1.26.2’
* 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  6.2Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      4.0Mb
* 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘parallel:::cleanup’ ‘parallel:::prepareCleanup’
  ‘parallel:::processID’ ‘parallel:::readChild’
  ‘parallel:::selectChildren’
  See the note in ?`:::` about the use of this operator.
* 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 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 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/SeqArray.Rcheck/00check.log’
for details.



Installation output

SeqArray.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL SeqArray
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘SeqArray’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DUSING_R -I"/home/biocbuild/bbs-3.10-bioc/R/library/gdsfmt/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DUSING_R -I"/home/biocbuild/bbs-3.10-bioc/R/library/gdsfmt/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c ConvToGDS.cpp -o ConvToGDS.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DUSING_R -I"/home/biocbuild/bbs-3.10-bioc/R/library/gdsfmt/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DUSING_R -I"/home/biocbuild/bbs-3.10-bioc/R/library/gdsfmt/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c FileMerge.cpp -o FileMerge.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DUSING_R -I"/home/biocbuild/bbs-3.10-bioc/R/library/gdsfmt/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c GetData.cpp -o GetData.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DUSING_R -I"/home/biocbuild/bbs-3.10-bioc/R/library/gdsfmt/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c Index.cpp -o Index.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DUSING_R -I"/home/biocbuild/bbs-3.10-bioc/R/library/gdsfmt/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c LinkSNPRelate.cpp -o LinkSNPRelate.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DUSING_R -I"/home/biocbuild/bbs-3.10-bioc/R/library/gdsfmt/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c Methods.cpp -o Methods.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DUSING_R -I"/home/biocbuild/bbs-3.10-bioc/R/library/gdsfmt/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c R_SeqArray.c -o R_SeqArray.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DUSING_R -I"/home/biocbuild/bbs-3.10-bioc/R/library/gdsfmt/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c ReadBySample.cpp -o ReadBySample.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DUSING_R -I"/home/biocbuild/bbs-3.10-bioc/R/library/gdsfmt/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c ReadByVariant.cpp -o ReadByVariant.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DUSING_R -I"/home/biocbuild/bbs-3.10-bioc/R/library/gdsfmt/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c SeqArray.cpp -o SeqArray.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DUSING_R -I"/home/biocbuild/bbs-3.10-bioc/R/library/gdsfmt/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c pkg_test.cpp -o pkg_test.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DUSING_R -I"/home/biocbuild/bbs-3.10-bioc/R/library/gdsfmt/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c samtools_ext.c -o samtools_ext.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DUSING_R -I"/home/biocbuild/bbs-3.10-bioc/R/library/gdsfmt/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c vectorization.c -o vectorization.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.10-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 ReadByVariant.o SeqArray.o pkg_test.o samtools_ext.o vectorization.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-SeqArray/00new/SeqArray/libs
** R
** data
** 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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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, which.max, which.min

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

Attaching package: 'S4Vectors'

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

    expand.grid

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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians

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

    rowRanges

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    rowRanges

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

    aperm, apply, rowsum


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, 8s

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

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

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

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 7s

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 2s
# 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 -- Wed Apr 15 01:44:29 2020 
*********************************************** 
Number of test functions: 27 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
SeqArray RUnit Tests - 27 test functions, 0 errors, 0 failures
Number of test functions: 27 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 82.892  43.336 123.391 

Example timings

SeqArray.Rcheck/SeqArray-Ex.timings

nameusersystemelapsed
SeqArray-package0.3200.0360.544
SeqVarGDSClass-class0.1440.0080.154
seqAddValue0.1000.0120.110
seqAlleleFreq0.0440.0000.046
seqApply0.1320.0120.146
seqAsVCF0.0040.0000.003
seqBED2GDS0.2600.0320.383
seqBlockApply0.0400.0000.041
seqCheck0.0240.0040.027
seqDelete0.0400.0040.044
seqDigest0.0240.0000.026
seqExampleFileName0.0000.0000.001
seqExport0.6800.1960.880
seqGDS2SNP0.0840.0080.093
seqGDS2VCF0.7680.0200.791
seqGetData0.0680.0040.074
seqGetFilter0.0440.0000.043
seqMerge1.1000.0441.153
seqMissing0.0560.0000.057
seqNumAllele0.0040.0000.005
seqOpen0.0360.0040.042
seqOptimize0.1520.0160.166
seqParallel0.1000.2040.195
seqParallelSetup0.0400.0560.078
seqRecompress1.2920.0681.323
seqResetVariantID0.0200.0160.035
seqSNP2GDS1.9320.0722.075
seqSetFilter0.0640.0120.077
seqSetFilterCond0.0440.0080.054
seqStorageOption0.5880.0640.653
seqSummary0.1480.0120.162
seqSystem000
seqTranspose0.1840.0160.202
seqVCF2GDS0.6000.1720.659
seqVCF_Header0.0720.0080.080
seqVCF_SampID0.0000.0000.002