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CHECK report for h5vc on tokay1

This page was generated on 2019-04-13 11:23:24 -0400 (Sat, 13 Apr 2019).

Package 705/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
h5vc 2.16.0
Paul Theodor Pyl
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/h5vc
Branch: RELEASE_3_8
Last Commit: fd6bd12
Last Changed Date: 2018-10-30 11:41:52 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: h5vc
Version: 2.16.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:h5vc.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings h5vc_2.16.0.tar.gz
StartedAt: 2019-04-13 02:58:40 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 03:05:03 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 383.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: h5vc.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:h5vc.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings h5vc_2.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/h5vc.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '2.16.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp6BVR53/R.INSTALL1dd8cfa1179/h5vc/man/geom_h5vc.Rd:25: file link 'geom_rect' in package 'ggplot2' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/h5vc.Rcheck/00install.out' for details.
* 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
* 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 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-3.8-bioc/R/library/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 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
callVariantsFisher 12.88   0.35   13.22
applyTallies       10.63   0.56   30.39
writeToTallyFile    6.65   0.47    7.13
mismatchPlot        5.86   0.49    6.35
binnedAFs           3.41   1.05    5.08
coverage            3.54   0.40    5.33
tallyRanges         3.58   0.27    5.42
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
applyTallies       12.08   0.51   33.71
callVariantsFisher 11.53   0.09   11.63
writeToTallyFile    5.56   0.58    6.14
mismatchPlot        5.15   0.06    5.22
* 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: 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/h5vc.Rcheck/00check.log'
for details.



Installation output

h5vc.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/h5vc_2.16.0.tar.gz && rm -rf h5vc.buildbin-libdir && mkdir h5vc.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=h5vc.buildbin-libdir h5vc_2.16.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL h5vc_2.16.0.zip && rm h5vc_2.16.0.tar.gz h5vc_2.16.0.zip
###
##############################################################################
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  242k  100  242k    0     0  5950k      0 --:--:-- --:--:-- --:--:-- 6566k

install for i386

* installing *source* package 'h5vc' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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-3.8-bioc/R/library/Rsamtools/usrlib/i386/libbam.a C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib/i386/libbam.a C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib/i386/libbcf.a C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -pthread -LC:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/h5vc.buildbin-libdir/h5vc/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'h5vc'
    finding HTML links ... done
    applyTallies                            html  
    batchTallies                            html  
    binGenome                               html  
    binnedAFs                               html  
    callVariants                            html  
    callVariantsFisher                      html  
    callVariantsSingle                      html  
    coverage                                html  
    geom_h5vc                               html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp6BVR53/R.INSTALL1dd8cfa1179/h5vc/man/geom_h5vc.Rd:25: file link 'geom_rect' in package 'ggplot2' does not exist and so has been treated as a topic
    getSampleData                           html  
    h5dapply                                html  
    h5readBlock                             html  
    h5vc-package                            html  
    helpers                                 html  
    mergeTallies                            html  
    mergeTallyFiles                         html  
    mismatchPlot                            html  
    mutationSpectrum                        html  
    plotMutationSpectrum                    html  
    prepareForHDF5                          html  
    prepareTallyFile                        html  
    tallyBAM                                html  
    tallyRanges                             html  
    finding level-2 HTML links ... done

    writeReference                          html  
    writeToTallyFile                        html  
** building package indices
** installing vignettes
   'h5vc.simple.genome.browser.Rmd' 
   'h5vc.tour.Rmd' 
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'h5vc' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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-3.8-bioc/R/library/Rsamtools/usrlib/x64/libbam.a C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib/x64/libbam.a C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib/x64/libbcf.a C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -pthread -LC:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/h5vc.buildbin-libdir/h5vc/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'h5vc' as h5vc_2.16.0.zip
* DONE (h5vc)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'h5vc' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

h5vc.Rcheck/tests_i386/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 -- Sat Apr 13 03:04:49 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 
   4.20    0.26    4.45 

h5vc.Rcheck/tests_x64/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 -- Sat Apr 13 03:04:54 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 
   4.50    0.34    4.81 

Example timings

h5vc.Rcheck/examples_i386/h5vc-Ex.timings

nameusersystemelapsed
applyTallies10.63 0.5630.39
batchTallies000
binGenome0.190.030.22
binnedAFs3.411.055.08
callVariants0.790.421.68
callVariantsFisher12.88 0.3513.22
callVariantsSingle1.260.471.74
coverage3.540.405.33
geom_h5vc0.670.110.78
getSampleData0.080.000.08
h5dapply1.270.031.30
h5readBlock0.250.000.97
helpers0.110.000.11
mergeTallies1.010.031.04
mergeTallyFiles000
mismatchPlot5.860.496.35
mutationSpectrum1.000.233.56
plotMutationSpectrum2.330.212.54
prepareForHDF50.730.010.75
prepareTallyFile0.120.000.12
tallyBAM0.130.000.13
tallyRanges3.580.275.42
writeReference0.230.010.25
writeToTallyFile6.650.477.13

h5vc.Rcheck/examples_x64/h5vc-Ex.timings

nameusersystemelapsed
applyTallies12.08 0.5133.71
batchTallies000
binGenome0.220.010.23
binnedAFs3.220.133.34
callVariants0.770.030.80
callVariantsFisher11.53 0.0911.63
callVariantsSingle1.120.081.20
coverage3.660.283.94
geom_h5vc0.690.040.72
getSampleData0.070.000.07
h5dapply1.040.121.16
h5readBlock0.230.020.25
helpers0.110.000.11
mergeTallies0.830.000.83
mergeTallyFiles000
mismatchPlot5.150.065.22
mutationSpectrum1.750.282.03
plotMutationSpectrum1.590.331.92
prepareForHDF50.640.140.79
prepareTallyFile0.140.000.14
tallyBAM0.110.000.11
tallyRanges3.780.234.01
writeReference0.30.00.3
writeToTallyFile5.560.586.14