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) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:23:24 -0400 (Sat, 13 Apr 2019).
| Package 705/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| h5vc 2.16.0 Paul Theodor Pyl
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| 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 |
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### Running command:
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### 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
###
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* 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.
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
|
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
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h5vc.Rcheck/examples_i386/h5vc-Ex.timings
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h5vc.Rcheck/examples_x64/h5vc-Ex.timings
|