Xiuwen Zheng
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/SeqArray |
| Branch: master |
| Last Commit: 08f03c8 |
| Last Changed Date: 2020-01-08 12:44:52 -0500 (Wed, 08 Jan 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:36:43 -0500 (Thu, 16 Jan 2020).
| Package 1555/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SeqArray 1.27.7 Xiuwen Zheng
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: SeqArray |
| Version: 1.27.7 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SeqArray.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SeqArray_1.27.7.tar.gz |
| StartedAt: 2020-01-16 08:46:22 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 08:51:35 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 312.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SeqArray.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SeqArray.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SeqArray_1.27.7.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/SeqArray.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.27.7’
* 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 ... OK
* 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 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
‘/Users/biocbuild/bbs-3.11-bioc/meat/SeqArray.Rcheck/00check.log’
for details.
SeqArray.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SeqArray ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘SeqArray’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/gdsfmt/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/gdsfmt/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ConvToGDS.cpp -o ConvToGDS.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/gdsfmt/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/gdsfmt/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c FileMerge.cpp -o FileMerge.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/gdsfmt/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c GetData.cpp -o GetData.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/gdsfmt/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c Index.cpp -o Index.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/gdsfmt/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c LinkSNPRelate.cpp -o LinkSNPRelate.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/gdsfmt/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c Methods.cpp -o Methods.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/gdsfmt/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c R_SeqArray.c -o R_SeqArray.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/gdsfmt/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ReadBySample.cpp -o ReadBySample.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/gdsfmt/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ReadByUnit.cpp -o ReadByUnit.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/gdsfmt/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ReadByVariant.cpp -o ReadByVariant.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/gdsfmt/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c SeqArray.cpp -o SeqArray.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/gdsfmt/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c pkg_test.cpp -o pkg_test.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/gdsfmt/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c samtools_ext.c -o samtools_ext.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/gdsfmt/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c vectorization.c -o vectorization.o clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/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)
SeqArray.Rcheck/tests/test.Rout
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, 4s
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 3s
[..................................................] 0%, ETC: ---
[=>................................................] 1%, ETC: 10.4m
[==================================================] 100%, completed, 8s
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
# of selected variants: 655
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 2s
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
[..................................................] 0%, ETC: ---
[=>................................................] 2%, ETC: 10.0m
[==================================================] 100%, completed, 7s
[..................................................] 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 Jan 16 08:51:23 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
91.635 26.506 118.507
SeqArray.Rcheck/SeqArray-Ex.timings
| name | user | system | elapsed | |
| SeqArray-package | 0.723 | 0.193 | 0.928 | |
| SeqVarGDSClass-class | 0.247 | 0.049 | 0.297 | |
| seqAddValue | 0.204 | 0.094 | 0.299 | |
| seqAlleleFreq | 0.055 | 0.006 | 0.060 | |
| seqApply | 0.179 | 0.031 | 0.210 | |
| seqAsVCF | 0.004 | 0.002 | 0.007 | |
| seqBED2GDS | 0.449 | 0.164 | 0.617 | |
| seqBlockApply | 0.091 | 0.018 | 0.109 | |
| seqCheck | 0.045 | 0.006 | 0.051 | |
| seqDelete | 0.099 | 0.015 | 0.117 | |
| seqDigest | 0.035 | 0.005 | 0.040 | |
| seqExampleFileName | 0.003 | 0.001 | 0.004 | |
| seqExport | 1.117 | 1.768 | 2.889 | |
| seqGDS2SNP | 0.111 | 0.147 | 0.259 | |
| seqGDS2VCF | 0.782 | 0.073 | 0.861 | |
| seqGetData | 0.091 | 0.015 | 0.106 | |
| seqGetFilter | 0.067 | 0.007 | 0.074 | |
| seqMerge | 1.427 | 0.334 | 1.769 | |
| seqMissing | 0.070 | 0.005 | 0.075 | |
| seqNumAllele | 0.006 | 0.003 | 0.010 | |
| seqOpen | 0.057 | 0.005 | 0.063 | |
| seqOptimize | 0.258 | 0.061 | 0.322 | |
| seqParallel | 0.304 | 0.317 | 0.393 | |
| seqParallelSetup | 0.107 | 0.093 | 0.165 | |
| seqRecompress | 0.418 | 0.220 | 0.650 | |
| seqResetVariantID | 0.043 | 0.049 | 0.095 | |
| seqSNP2GDS | 1.999 | 0.346 | 2.366 | |
| seqSetFilter | 0.135 | 0.042 | 0.178 | |
| seqSetFilterCond | 0.099 | 0.025 | 0.125 | |
| seqStorageOption | 0.909 | 0.257 | 1.171 | |
| seqSummary | 0.303 | 0.060 | 0.363 | |
| seqSystem | 0.001 | 0.000 | 0.001 | |
| seqTranspose | 0.261 | 0.047 | 0.309 | |
| seqUnitApply | 0.660 | 0.339 | 0.795 | |
| seqUnitSlidingWindows | 0.053 | 0.015 | 0.068 | |
| seqVCF2GDS | 1.017 | 0.568 | 1.391 | |
| seqVCF_Header | 0.133 | 0.027 | 0.159 | |
| seqVCF_SampID | 0.003 | 0.002 | 0.005 | |