Paul Theodor Pyl
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/h5vc |
| Branch: RELEASE_3_7 |
| Last Commit: 21b4607 |
| Last Changed Date: 2018-04-30 10:35:31 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:25:41 -0400 (Wed, 17 Oct 2018).
| Package 670/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| h5vc 2.14.0 Paul Theodor Pyl
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: h5vc |
| Version: 2.14.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:h5vc.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings h5vc_2.14.0.tar.gz |
| StartedAt: 2018-10-16 01:05:25 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 01:07:45 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 139.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: h5vc.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:h5vc.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings h5vc_2.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/h5vc.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘h5vc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘h5vc’ version ‘2.14.0’
* 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 ‘h5vc’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.h5dapplyIRanges: no visible binding for global variable ‘Sample’
binnedAFs : <anonymous>: no visible global function definition for
‘hist’
callVariantsPaired : <anonymous> : <anonymous>: no visible global
function definition for ‘binom.test’
callVariantsPairedFisher : <anonymous> : <anonymous> : <anonymous>: no
visible global function definition for ‘fisher.test’
callVariantsPairedFisher : <anonymous> : <anonymous>: no visible
binding for global variable ‘pValue’
callVariantsPairedFisher : <anonymous> : <anonymous>: no visible
binding for global variable ‘BlockID’
callVariantsSingle : <anonymous> : <anonymous>: no visible binding for
global variable ‘Support’
callVariantsSingle : <anonymous> : <anonymous>: no visible binding for
global variable ‘AF’
callVariantsSingle : <anonymous> : <anonymous>: no visible binding for
global variable ‘SupFwd’
callVariantsSingle : <anonymous> : <anonymous>: no visible binding for
global variable ‘SupRev’
callVariantsSingle : <anonymous> : <anonymous> : binom.test.safe: no
visible global function definition for ‘binom.test’
callVariantsSingle : <anonymous> : <anonymous> : <anonymous>: no
visible global function definition for ‘fisher.test’
callVariantsSingle : <anonymous> : <anonymous>: no visible binding for
global variable ‘BlockID’
mergeTallyFiles : <anonymous>: no visible binding for global variable
‘group’
mergeTallyFiles: no visible binding for global variable ‘SourceFile’
mismatchPlot: no visible binding for global variable ‘Sample’
plotMutationSpectrum: no visible binding for global variable
‘altAllele’
plotMutationSpectrum: no visible binding for global variable ‘tmp’
rerunBatchTallies: no visible binding for global variable ‘regID’
resizeCohort: no visible binding for global variable ‘newSamples’
tallyRangesBatch : <anonymous>: no visible binding for global variable
‘bamFiles’
tallyRangesBatch: no visible binding for global variable ‘verbose’
Undefined global functions or variables:
AF BlockID Sample SourceFile SupFwd SupRev Support altAllele bamFiles
binom.test fisher.test group hist newSamples pValue regID tmp verbose
Consider adding
importFrom("graphics", "hist")
importFrom("stats", "binom.test", "fisher.test")
to your NAMESPACE file.
* 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 ‘/home/biocbuild/bbs-3.7-bioc/R/library/h5vc/libs/h5vc.so’:
Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Found ‘stderr’, possibly from ‘stderr’ (C)
Found ‘stdout’, possibly from ‘stdout’ (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
callVariantsFisher 10.584 0.016 10.611
applyTallies 7.852 1.668 9.133
writeToTallyFile 5.820 1.392 6.777
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.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-3.7-bioc/meat/h5vc.Rcheck/00check.log’
for details.
h5vc.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL h5vc
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘h5vc’ ...
** libs
g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I/usr/local/include -fpic -g -O2 -Wall -c tallyBAM.cpp -o tallyBAM.o
tallyBAM.cpp: In function ‘int pileup_func_old(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)’:
tallyBAM.cpp:47:7: warning: unused variable ‘len’ [-Wunused-variable]
int len = nttable->end - nttable->beg;
^
tallyBAM.cpp: In function ‘int pileup_func(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)’:
tallyBAM.cpp:96:7: warning: unused variable ‘len’ [-Wunused-variable]
int len = nttable->end - nttable->beg;
^
tallyBAM.cpp: In function ‘int _tallyBAM(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*)’:
tallyBAM.cpp:141:6: warning: unused variable ‘c’ [-Wunused-variable]
int c = 0;
^
tallyBAM.cpp: At global scope:
tallyBAM.cpp:43:12: warning: ‘int pileup_func_old(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)’ defined but not used [-Wunused-function]
static int pileup_func_old(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data)
^
g++ -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o h5vc.so tallyBAM.o /home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/h5vc/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
‘h5vc.simple.genome.browser.Rmd’
‘h5vc.tour.Rmd’
** testing if installed package can be loaded
* DONE (h5vc)
h5vc.Rcheck/tests/runTests.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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.
> BiocGenerics:::testPackage("h5vc")
RUNIT TEST PROTOCOL -- Tue Oct 16 01:07:42 2018
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
h5vc RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
3.684 0.176 3.871
h5vc.Rcheck/h5vc-Ex.timings
| name | user | system | elapsed | |
| applyTallies | 7.852 | 1.668 | 9.133 | |
| batchTallies | 0.000 | 0.000 | 0.001 | |
| binGenome | 0.208 | 0.000 | 0.266 | |
| binnedAFs | 3.008 | 0.152 | 3.324 | |
| callVariants | 0.752 | 0.000 | 0.771 | |
| callVariantsFisher | 10.584 | 0.016 | 10.611 | |
| callVariantsSingle | 1.080 | 0.000 | 1.082 | |
| coverage | 3.152 | 0.036 | 3.251 | |
| geom_h5vc | 0.704 | 0.000 | 0.719 | |
| getSampleData | 0.052 | 0.000 | 0.052 | |
| h5dapply | 0.916 | 0.016 | 0.932 | |
| h5readBlock | 0.268 | 0.000 | 0.468 | |
| helpers | 0.148 | 0.000 | 0.149 | |
| mergeTallies | 0.844 | 0.012 | 0.854 | |
| mergeTallyFiles | 0.000 | 0.000 | 0.001 | |
| mismatchPlot | 4.804 | 0.016 | 4.844 | |
| mutationSpectrum | 0.692 | 0.120 | 0.899 | |
| plotMutationSpectrum | 2.136 | 0.060 | 2.197 | |
| prepareForHDF5 | 0.576 | 0.004 | 0.579 | |
| prepareTallyFile | 0.112 | 0.000 | 0.114 | |
| tallyBAM | 0.040 | 0.000 | 0.037 | |
| tallyRanges | 2.332 | 0.912 | 4.541 | |
| writeReference | 0.244 | 0.016 | 0.258 | |
| writeToTallyFile | 5.820 | 1.392 | 6.777 | |