Paul Theodor Pyl
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/h5vc |
| Branch: master |
| Last Commit: 6de5b78 |
| Last Changed Date: 2019-02-12 10:46:29 -0400 (Tue, 12 Feb 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:28:55 -0400 (Tue, 09 Apr 2019).
| Package 728/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| h5vc 2.17.1 Paul Theodor Pyl
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | ERROR | skipped | skipped | |||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
| Package: h5vc |
| Version: 2.17.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:h5vc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings h5vc_2.17.1.tar.gz |
| StartedAt: 2019-04-09 01:26:56 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 01:30:43 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 226.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: h5vc.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:h5vc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings h5vc_2.17.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/h5vc.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.17.1’
* 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 ... NOTE
Versioned 'LinkingTo' value for ‘Rhtslib’ is only usable in R >= 3.0.2
* 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 ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/h5vc/libs/h5vc.so’:
Found ‘___assert_rtn’, possibly from ‘assert’ (C)
Found ‘___stderrp’, possibly from ‘stderr’ (C)
Found ‘___stdoutp’, possibly from ‘stdout’ (C)
Found ‘_abort’, possibly from ‘abort’ (C)
Found ‘_exit’, possibly from ‘exit’ (C)
Found ‘_printf’, possibly from ‘printf’ (C)
Found ‘_putchar’, possibly from ‘putchar’ (C)
Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Found ‘_srand48’, possibly from ‘srand48’ (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 18.784 0.524 19.500
applyTallies 13.089 2.686 15.640
writeToTallyFile 8.767 2.786 10.580
tallyRanges 5.725 2.498 7.266
mismatchPlot 5.955 0.323 6.334
plotMutationSpectrum 4.780 1.389 6.230
mutationSpectrum 4.268 1.142 5.463
binnedAFs 4.630 0.664 5.363
coverage 4.590 0.374 5.016
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/h5vc.Rcheck/00check.log’
for details.
h5vc.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL h5vc
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘h5vc’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/Library/Frameworks/R.framework/Resources/bin/R" --vanilla --slave` -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c bam.c -o bam.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/Library/Frameworks/R.framework/Resources/bin/R" --vanilla --slave` -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c bam_plbuf.c -o bam_plbuf.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/Library/Frameworks/R.framework/Resources/bin/R" --vanilla --slave` -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c sam.c -o sam.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/Library/Frameworks/R.framework/Resources/bin/R" --vanilla --slave` -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c tallyBAM.cpp -o tallyBAM.o
tallyBAM.cpp:47:7: warning: unused variable 'len' [-Wunused-variable]
int len = nttable->end - nttable->beg;
^
tallyBAM.cpp:60:18: warning: variable 'c' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
}else if(p->indel > 0){
^˜˜˜˜˜˜˜˜˜˜˜
tallyBAM.cpp:64:16: note: uninitialized use occurs here
str += c;
^
tallyBAM.cpp:60:15: note: remove the 'if' if its condition is always true
}else if(p->indel > 0){
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
tallyBAM.cpp:55:15: note: initialize the variable 'c' to silence this warning
char c;
^
= '\0'
tallyBAM.cpp:96:7: warning: unused variable 'len' [-Wunused-variable]
int len = nttable->end - nttable->beg;
^
tallyBAM.cpp:140:6: warning: unused variable 'c' [-Wunused-variable]
int c = 0;
^
tallyBAM.cpp:43:12: warning: unused function 'pileup_func_old' [-Wunused-function]
static int pileup_func_old(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data)
^
5 warnings generated.
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 h5vc.so bam.o bam_plbuf.o sam.o tallyBAM.o /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/usrlib/libhts.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/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 Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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.
> BiocGenerics:::testPackage("h5vc")
RUNIT TEST PROTOCOL -- Tue Apr 9 01:30:36 2019
***********************************************
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
5.842 0.434 6.313
h5vc.Rcheck/h5vc-Ex.timings
| name | user | system | elapsed | |
| applyTallies | 13.089 | 2.686 | 15.640 | |
| batchTallies | 0 | 0 | 0 | |
| binGenome | 0.243 | 0.088 | 0.334 | |
| binnedAFs | 4.630 | 0.664 | 5.363 | |
| callVariants | 0.857 | 0.213 | 1.101 | |
| callVariantsFisher | 18.784 | 0.524 | 19.500 | |
| callVariantsSingle | 1.425 | 0.241 | 1.680 | |
| coverage | 4.590 | 0.374 | 5.016 | |
| geom_h5vc | 0.914 | 0.056 | 0.977 | |
| getSampleData | 0.058 | 0.003 | 0.061 | |
| h5dapply | 1.344 | 0.060 | 1.415 | |
| h5readBlock | 0.266 | 0.028 | 0.296 | |
| helpers | 0.124 | 0.006 | 0.131 | |
| mergeTallies | 1.021 | 0.069 | 1.101 | |
| mergeTallyFiles | 0.000 | 0.000 | 0.001 | |
| mismatchPlot | 5.955 | 0.323 | 6.334 | |
| mutationSpectrum | 4.268 | 1.142 | 5.463 | |
| plotMutationSpectrum | 4.780 | 1.389 | 6.230 | |
| prepareForHDF5 | 1.041 | 0.053 | 1.103 | |
| prepareTallyFile | 0.136 | 0.004 | 0.142 | |
| tallyBAM | 0.064 | 0.006 | 0.070 | |
| tallyRanges | 5.725 | 2.498 | 7.266 | |
| writeReference | 0.322 | 0.060 | 0.386 | |
| writeToTallyFile | 8.767 | 2.786 | 10.580 | |