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BioC 3.5: CHECK report for h5vc on tokay2

This page was generated on 2017-10-18 14:23:04 -0400 (Wed, 18 Oct 2017).

Package 612/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
h5vc 2.10.0
Paul Theodor Pyl
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/h5vc
Branch: RELEASE_3_5
Last Commit: bb2f005
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: h5vc
Version: 2.10.0
Command: rm -rf h5vc.buildbin-libdir h5vc.Rcheck && mkdir h5vc.buildbin-libdir h5vc.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=h5vc.buildbin-libdir h5vc_2.10.0.tar.gz >h5vc.Rcheck\00install.out 2>&1 && cp h5vc.Rcheck\00install.out h5vc-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=h5vc.buildbin-libdir --install="check:h5vc-install.out" --force-multiarch --no-vignettes --timings h5vc_2.10.0.tar.gz
StartedAt: 2017-10-18 00:30:56 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 00:39:55 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 539.4 seconds
RetCode: 0
Status:  OK  
CheckDir: h5vc.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf h5vc.buildbin-libdir h5vc.Rcheck && mkdir h5vc.buildbin-libdir h5vc.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=h5vc.buildbin-libdir h5vc_2.10.0.tar.gz >h5vc.Rcheck\00install.out 2>&1 && cp h5vc.Rcheck\00install.out h5vc-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=h5vc.buildbin-libdir --install="check:h5vc-install.out" --force-multiarch --no-vignettes --timings h5vc_2.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/h5vc.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'h5vc/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'h5vc' version '2.10.0'
* 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 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
* loading checks for arch 'i386'
** 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 loading without being on the library search path ... OK
* loading checks for arch 'x64'
** 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 loading without being on the library search path ... 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.5-bioc/meat/h5vc.buildbin-libdir/h5vc/libs/i386/h5vc.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
  Found 'rand', possibly from 'rand' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
applyTallies       9.95   0.79   26.34
callVariantsFisher 9.62   0.19    9.81
writeToTallyFile   7.19   0.61    7.80
mismatchPlot       5.62   0.51    6.14
tallyRanges        5.76   0.33   30.56
binnedAFs          3.92   0.47    9.26
coverage           3.88   0.28    5.69
callVariants       2.02   0.12    6.04
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
callVariantsFisher 15.60   0.03   15.62
applyTallies       12.68   0.39   27.95
mismatchPlot       11.09   0.11   12.04
writeToTallyFile    7.42   0.48    7.90
binnedAFs           5.39   0.16    5.57
coverage            4.81   0.36    5.28
tallyRanges         4.80   0.24    5.03
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/h5vc.Rcheck/00check.log'
for details.


h5vc.Rcheck/00install.out:


install for i386

* installing *source* package 'h5vc' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -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)
            ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o h5vc.dll tmp.def tallyBAM.o C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/usrlib/i386/libbam.a C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/usrlib/i386/libbam.a C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/usrlib/i386/libbcf.a C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -pthread -LC:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/h5vc.buildbin-libdir/h5vc/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'h5vc' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -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)
            ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o h5vc.dll tmp.def tallyBAM.o C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/usrlib/x64/libbam.a C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/usrlib/x64/libbam.a C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/usrlib/x64/libbcf.a C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -pthread -LC:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/h5vc.buildbin-libdir/h5vc/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'h5vc' as h5vc_2.10.0.zip
* DONE (h5vc)

h5vc.Rcheck/examples_i386/h5vc-Ex.timings:

nameusersystemelapsed
applyTallies 9.95 0.7926.34
batchTallies000
binGenome0.520.020.53
binnedAFs3.920.479.26
callVariants2.020.126.04
callVariantsFisher9.620.199.81
callVariantsSingle1.220.281.50
coverage3.880.285.69
geom_h5vc1.530.061.59
getSampleData0.110.000.11
h5dapply1.280.051.33
h5readBlock0.290.000.78
helpers0.210.000.20
mergeTallies1.130.101.22
mergeTallyFiles000
mismatchPlot5.620.516.14
mutationSpectrum1.030.203.17
plotMutationSpectrum1.790.191.99
prepareForHDF50.750.050.79
prepareTallyFile0.10.00.1
tallyBAM0.110.000.11
tallyRanges 5.76 0.3330.56
writeReference0.360.000.36
writeToTallyFile7.190.617.80

h5vc.Rcheck/examples_x64/h5vc-Ex.timings:

nameusersystemelapsed
applyTallies12.68 0.3927.95
batchTallies000
binGenome0.730.080.81
binnedAFs5.390.165.57
callVariants2.310.072.39
callVariantsFisher15.60 0.0315.62
callVariantsSingle1.560.071.63
coverage4.810.365.28
geom_h5vc2.380.012.39
getSampleData0.090.000.12
h5dapply1.560.101.66
h5readBlock0.200.010.21
helpers0.210.000.21
mergeTallies1.340.021.36
mergeTallyFiles000
mismatchPlot11.09 0.1112.04
mutationSpectrum2.500.262.77
plotMutationSpectrum3.480.133.62
prepareForHDF51.440.031.55
prepareTallyFile0.200.000.41
tallyBAM0.170.010.19
tallyRanges4.800.245.03
writeReference0.470.030.58
writeToTallyFile7.420.487.90