Package: h5vc

Version: 2.16.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:h5vc.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings h5vc_2.16.0.tar.gz

StartedAt: 2019-04-16 00:33:04 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 00:36:42 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 218.2 seconds

RetCode: 0

Status:  OK

CheckDir: h5vc.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:h5vc.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings h5vc_2.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/h5vc.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘2.16.0’
* 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-3.8-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 17.504  0.000  17.679
applyTallies       10.060  1.248  11.462
writeToTallyFile    8.000  1.740   9.437
mismatchPlot        7.540  0.036   8.370
tallyRanges         4.688  1.400   6.606
coverage            4.688  0.080   5.476
* 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-3.8-bioc/meat/h5vc.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL h5vc
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘h5vc’ ...
** libs
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/lib -L/usr/local/lib -o h5vc.so tallyBAM.o /home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-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)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 Apr 16 00:36:33 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 
  5.984   0.180   6.688 

name	user	system	elapsed
applyTallies	10.060	1.248	11.462
batchTallies	0	0	0
binGenome	0.324	0.008	0.398
binnedAFs	4.508	0.172	4.997
callVariants	0.960	0.008	1.052
callVariantsFisher	17.504	0.000	17.679
callVariantsSingle	1.552	0.012	1.566
coverage	4.688	0.080	5.476
geom_h5vc	1.056	0.000	1.462
getSampleData	0.084	0.000	0.087
h5dapply	1.532	0.032	1.781
h5readBlock	0.284	0.000	0.388
helpers	0.188	0.000	0.188
mergeTallies	1.168	0.024	1.278
mergeTallyFiles	0	0	0
mismatchPlot	7.540	0.036	8.370
mutationSpectrum	1.260	0.104	1.913
plotMutationSpectrum	3.256	0.068	3.753
prepareForHDF5	1.924	0.012	2.076
prepareTallyFile	0.192	0.004	0.329
tallyBAM	0.060	0.000	0.127
tallyRanges	4.688	1.400	6.606
writeReference	0.340	0.016	0.355
writeToTallyFile	8.000	1.740	9.437