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This page was generated on 2021-10-15 15:05:52 -0400 (Fri, 15 Oct 2021).

CHECK results for SeqArray on nebbiolo1

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? here 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 1731/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SeqArray 1.32.0  (landing page)
Xiuwen Zheng
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/SeqArray
git_branch: RELEASE_3_13
git_last_commit: 8fa3c99
git_last_commit_date: 2021-05-19 11:58:07 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: SeqArray
Version: 1.32.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:SeqArray.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings SeqArray_1.32.0.tar.gz
StartedAt: 2021-10-14 11:34:34 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 11:37:45 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 191.4 seconds
RetCode: 0
Status:   OK  
CheckDir: SeqArray.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:SeqArray.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings SeqArray_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/SeqArray.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.32.0’
* 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  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      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 ... 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 ... 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 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/SeqArray.Rcheck/00check.log’
for details.



Installation output

SeqArray.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL SeqArray
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘SeqArray’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.13-bioc/R/library/gdsfmt/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c Methods.cpp -o Methods.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.13-bioc/R/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-3.13-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-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.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, 5s

[..................................................]  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, 4s

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

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 1s
# 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 -- Thu Oct 14 11:37:40 2021 
*********************************************** 
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 
There were 50 or more warnings (use warnings() to see the first 50)
> 
> proc.time()
   user  system elapsed 
 57.136  58.581  88.853 

Example timings

SeqArray.Rcheck/SeqArray-Ex.timings

nameusersystemelapsed
SeqArray-package0.2800.0960.379
SeqVarGDSClass-class0.1290.0170.145
seqAddValue0.1220.0280.150
seqAlleleFreq0.0560.0040.059
seqApply0.0920.0240.116
seqAsVCF0.0030.0000.003
seqBED2GDS0.2800.0360.318
seqBlockApply0.0460.0120.059
seqCheck0.0190.0080.027
seqDelete0.0620.0120.074
seqDigest0.0230.0000.024
seqExampleFileName0.0020.0000.002
seqExport0.7670.1800.947
seqGDS2SNP0.0710.0040.075
seqGDS2VCF0.4730.0080.481
seqGetData0.0580.0040.063
seqGetFilter0.0340.0070.040
seqMerge0.6110.1960.808
seqMissing0.0550.0040.059
seqNewVarData0.0000.0030.003
seqNumAllele0.0000.0040.004
seqOpen0.0220.0130.035
seqOptimize0.1290.0480.176
seqParallel0.1110.4140.277
seqParallelSetup0.0590.0900.104
seqRecompress0.5940.0850.611
seqResetVariantID0.0340.0230.058
seqSNP2GDS1.4850.0721.559
seqSetFilter0.0550.0240.080
seqSetFilterCond0.0390.0120.051
seqStorageOption0.4680.2980.767
seqSummary0.1100.0680.177
seqSystem0.0000.0000.001
seqTranspose0.1480.0770.226
seqUnitApply0.3510.1700.397
seqUnitFilterCond0.0510.0200.071
seqUnitSlidingWindows0.0340.0070.042
seqVCF2GDS0.4860.3270.650
seqVCF_Header0.0770.0040.081
seqVCF_SampID0.0030.0000.003