Paul Theodor Pyl
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/h5vc |
| Branch: RELEASE_3_6 |
| Last Commit: a7f1d34 |
| Last Changed Date: 2017-10-30 12:40:09 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:11:43 -0400 (Thu, 12 Apr 2018).
| Package 636/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| h5vc 2.12.0 Paul Theodor Pyl
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: h5vc |
| Version: 2.12.0 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings h5vc_2.12.0.tar.gz |
| StartedAt: 2018-04-12 00:12:24 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 00:15:12 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 167.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: h5vc.Rcheck |
| Warnings: 0 |
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###
### Running command:
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### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings h5vc_2.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/h5vc.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘2.12.0’
* 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 ... OK
* 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 10.832 0.016 10.857
applyTallies 6.164 0.600 8.891
mismatchPlot 6.480 0.020 6.555
writeToTallyFile 5.324 0.520 7.994
tallyRanges 2.100 0.372 5.015
* 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: 1 NOTE
See
‘/home/biocbuild/bbs-3.6-bioc/meat/h5vc.Rcheck/00check.log’
for details.
h5vc.Rcheck/00install.out
* installing *source* package ‘h5vc’ ...
** libs
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/lib -L/usr/local/lib -o h5vc.so tallyBAM.o /home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/h5vc.Rcheck/h5vc/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (h5vc)
h5vc.Rcheck/tests/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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 -- Thu Apr 12 00:15:08 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
4.512 0.072 4.585
h5vc.Rcheck/h5vc-Ex.timings
| name | user | system | elapsed | |
| applyTallies | 6.164 | 0.600 | 8.891 | |
| batchTallies | 0.000 | 0.000 | 0.001 | |
| binGenome | 0.492 | 0.032 | 0.582 | |
| binnedAFs | 3.664 | 0.040 | 3.910 | |
| callVariants | 1.556 | 0.004 | 1.783 | |
| callVariantsFisher | 10.832 | 0.016 | 10.857 | |
| callVariantsSingle | 1.368 | 0.008 | 1.378 | |
| coverage | 3.348 | 0.024 | 3.446 | |
| geom_h5vc | 1.904 | 0.004 | 1.915 | |
| getSampleData | 0.060 | 0.000 | 0.057 | |
| h5dapply | 1.068 | 0.004 | 1.072 | |
| h5readBlock | 0.284 | 0.004 | 0.565 | |
| helpers | 0.232 | 0.004 | 0.235 | |
| mergeTallies | 1.036 | 0.004 | 1.043 | |
| mergeTallyFiles | 0.004 | 0.000 | 0.001 | |
| mismatchPlot | 6.480 | 0.020 | 6.555 | |
| mutationSpectrum | 0.956 | 0.172 | 1.457 | |
| plotMutationSpectrum | 1.828 | 0.072 | 1.902 | |
| prepareForHDF5 | 0.824 | 0.020 | 0.848 | |
| prepareTallyFile | 0.100 | 0.004 | 0.105 | |
| tallyBAM | 0.04 | 0.00 | 0.04 | |
| tallyRanges | 2.100 | 0.372 | 5.015 | |
| writeReference | 0.864 | 0.080 | 0.948 | |
| writeToTallyFile | 5.324 | 0.520 | 7.994 | |