Altuna Akalin
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/methylKit |
| Branch: RELEASE_3_7 |
| Last Commit: fd2779b |
| Last Changed Date: 2018-10-11 16:55:12 -0400 (Thu, 11 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:42:34 -0400 (Wed, 17 Oct 2018).
| Package 889/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| methylKit 1.6.3 Altuna Akalin
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: methylKit |
| Version: 1.6.3 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methylKit.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings methylKit_1.6.3.tar.gz |
| StartedAt: 2018-10-17 03:15:33 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 03:22:33 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 420.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: methylKit.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methylKit.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings methylKit_1.6.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/methylKit.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'methylKit/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'methylKit' version '1.6.3'
* 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 'methylKit' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/calculateDiffMeth-methods.Rd:179: file link 'pool' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/calculateDiffMeth-methods.Rd:179: file link 'reorganize' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/calculateDiffMeth-methods.Rd:180: file link 'dataSim' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/extract-methods.Rd:38: file link 'getData' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/joinSegmentNeighbours.Rd:10: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/joinSegmentNeighbours.Rd:14: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methSeg.Rd:11: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methSeg.Rd:14: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methSeg.Rd:39: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methSeg2bed.Rd:13: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylBase-class.Rd:63: file link 'getData' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylBase-class.Rd:63: file link 'getAssembly' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylBase-class.Rd:64: file link 'getContext' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylBase-class.Rd:70: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylBaseDB-class.Rd:69: file link 'getData' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylBaseDB-class.Rd:69: file link 'getAssembly' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylBaseDB-class.Rd:70: file link 'getContext' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylBaseDB-class.Rd:76: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylDiff-class.Rd:11: file link 'calculateDiffMeth' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylDiff-class.Rd:49: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylDiff-class.Rd:55: file link 'getData' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylDiff-class.Rd:55: file link 'getAssembly' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylDiff-class.Rd:56: file link 'getContext' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylDiffDB-class.Rd:11: file link 'calculateDiffMeth' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylDiffDB-class.Rd:52: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylDiffDB-class.Rd:59: file link 'getData' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylDiffDB-class.Rd:59: file link 'getAssembly' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylDiffDB-class.Rd:60: file link 'getContext' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRaw-class.Rd:41: file link 'getData' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRaw-class.Rd:41: file link 'getAssembly' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRaw-class.Rd:42: file link 'getContext' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRaw-class.Rd:48: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRawDB-class.Rd:47: file link 'getData' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRawDB-class.Rd:47: file link 'getAssembly' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRawDB-class.Rd:48: file link 'getContext' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRawDB-class.Rd:54: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRawList-class.Rd:9: file link 'methylRaw' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRawList-class.Rd:12: file link 'read' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRawListDB-class.Rd:9: file link 'methylRawDB' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRawListDB-class.Rd:12: file link 'read' in package 'methylKit' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/methylKit.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 5.5Mb
sub-directories of 1Mb or more:
R 1.2Mb
libs 2.6Mb
* 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 ... NOTE
Namespace in Imports field not imported from: 'KernSmooth'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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-3.7-bioc/R/library/methylKit/libs/i386/methylKit.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'putchar', possibly from 'putchar' (C)
Found 'puts', possibly from 'printf' (C), 'puts' (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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
calculateDiffMeth-methods 5.08 0.22 5.3
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
calculateDiffMeth-methods 5.45 0.17 5.63
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.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, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/methylKit.Rcheck/00check.log'
for details.
methylKit.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/methylKit_1.6.3.tar.gz && rm -rf methylKit.buildbin-libdir && mkdir methylKit.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=methylKit.buildbin-libdir methylKit_1.6.3.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL methylKit_1.6.3.zip && rm methylKit_1.6.3.tar.gz methylKit_1.6.3.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 624k 100 624k 0 0 11.8M 0 --:--:-- --:--:-- --:--:-- 13.5M
install for i386
* installing *source* package 'methylKit' ...
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c methCall.cpp -o methCall.o
methCall.cpp: In function 'int process_sam(std::istream*, std::string&, std::string&, std::string&, int&, int&, int&, int, int)':
methCall.cpp:708:84: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
^
methCall.cpp:707:84: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
^
methCall.cpp:706:81: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CpGstatus) { processCGmethHash(CGmethHash,out,mincov); std::fclose(out); }
^
methCall.cpp: In function 'int process_bam(std::string&, std::string&, std::string&, std::string&, int&, int&, int&, int)':
methCall.cpp:1027:84: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
^
methCall.cpp:1026:84: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
^
methCall.cpp:1025:81: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CpGstatus) { processCGmethHash(CGmethHash,out,mincov); std::fclose(out); }
^
methCall.cpp: In function 'int process_single_bismark(std::istream*, std::string&, std::string&, std::string&, int&, int&, int&)':
methCall.cpp:1254:84: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
^
methCall.cpp:1253:84: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
^
methCall.cpp:1252:81: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CpGstatus) { processCGmethHash(CGmethHash,out,mincov); std::fclose(out); }
^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o methylKit.dll tmp.def RcppExports.o methCall.o -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/usrlib/i386 -lhts -lz -lm -lws2_32 -lpthread -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/methylKit.buildbin-libdir/methylKit/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'methylKit'
finding HTML links ... done
PCASamples-methods html
adjustMethylC html
assocComp-methods html
bedgraph-methods html
calculateDiffMeth-methods html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/calculateDiffMeth-methods.Rd:179: file link 'pool' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/calculateDiffMeth-methods.Rd:179: file link 'reorganize' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/calculateDiffMeth-methods.Rd:180: file link 'dataSim' in package 'methylKit' does not exist and so has been treated as a topic
calculateDiffMethDSS-methods html
clusterSamples-methods html
dataSim-methods html
diffMethPerChr-methods html
extract-methods html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/extract-methods.Rd:38: file link 'getData' in package 'methylKit' does not exist and so has been treated as a topic
filterByCoverage-methods html
genomation-deprecated html
getAssembly-methods html
getContext-methods html
getCorrelation-methods html
getCoverageStats-methods html
getDBPath-methods html
getData-methods html
getMethylDiff-methods html
getMethylationStats-methods html
getSampleID-methods html
getTreatment-methods html
joinSegmentNeighbours html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/joinSegmentNeighbours.Rd:10: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/joinSegmentNeighbours.Rd:14: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
makeMethylDB-methods html
methRead-methods html
methSeg html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methSeg.Rd:11: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methSeg.Rd:14: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methSeg.Rd:39: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
methSeg2bed html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methSeg2bed.Rd:13: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
methylBase-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylBase-class.Rd:63: file link 'getData' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylBase-class.Rd:63: file link 'getAssembly' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylBase-class.Rd:64: file link 'getContext' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylBase-class.Rd:70: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
methylBase.obj html
methylBaseDB-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylBaseDB-class.Rd:69: file link 'getData' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylBaseDB-class.Rd:69: file link 'getAssembly' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylBaseDB-class.Rd:70: file link 'getContext' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylBaseDB-class.Rd:76: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
methylDiff-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylDiff-class.Rd:11: file link 'calculateDiffMeth' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylDiff-class.Rd:49: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylDiff-class.Rd:55: file link 'getData' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylDiff-class.Rd:55: file link 'getAssembly' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylDiff-class.Rd:56: file link 'getContext' in package 'methylKit' does not exist and so has been treated as a topic
methylDiff.obj html
methylDiffDB-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylDiffDB-class.Rd:11: file link 'calculateDiffMeth' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylDiffDB-class.Rd:52: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylDiffDB-class.Rd:59: file link 'getData' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylDiffDB-class.Rd:59: file link 'getAssembly' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylDiffDB-class.Rd:60: file link 'getContext' in package 'methylKit' does not exist and so has been treated as a topic
methylRaw-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRaw-class.Rd:41: file link 'getData' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRaw-class.Rd:41: file link 'getAssembly' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRaw-class.Rd:42: file link 'getContext' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRaw-class.Rd:48: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
methylRawDB-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRawDB-class.Rd:47: file link 'getData' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRawDB-class.Rd:47: file link 'getAssembly' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRawDB-class.Rd:48: file link 'getContext' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRawDB-class.Rd:54: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
methylRawList-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRawList-class.Rd:9: file link 'methylRaw' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRawList-class.Rd:12: file link 'read' in package 'methylKit' does not exist and so has been treated as a topic
methylRawList.obj html
methylRawListDB-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRawListDB-class.Rd:9: file link 'methylRawDB' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRawListDB-class.Rd:12: file link 'read' in package 'methylKit' does not exist and so has been treated as a topic
normalizeCoverage-methods html
percMethylation-methods html
pool-methods html
processBismarkAln-methods html
reconstruct-methods html
regionCounts html
finding level-2 HTML links ... done
removeComp-methods html
reorganize-methods html
select-methods html
selectByOverlap-methods html
show-methods html
tileMethylCounts-methods html
unite-methods html
updateMethObject html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'methylKit' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c methCall.cpp -o methCall.o
methCall.cpp: In function 'int process_sam(std::istream*, std::string&, std::string&, std::string&, int&, int&, int&, int, int)':
methCall.cpp:708:84: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
^
methCall.cpp:707:84: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
^
methCall.cpp:706:81: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CpGstatus) { processCGmethHash(CGmethHash,out,mincov); std::fclose(out); }
^
methCall.cpp: In function 'int process_bam(std::string&, std::string&, std::string&, std::string&, int&, int&, int&, int)':
methCall.cpp:1027:84: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
^
methCall.cpp:1026:84: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
^
methCall.cpp:1025:81: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CpGstatus) { processCGmethHash(CGmethHash,out,mincov); std::fclose(out); }
^
methCall.cpp: In function 'int process_single_bismark(std::istream*, std::string&, std::string&, std::string&, int&, int&, int&)':
methCall.cpp:1254:84: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
^
methCall.cpp:1253:84: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
^
methCall.cpp:1252:81: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CpGstatus) { processCGmethHash(CGmethHash,out,mincov); std::fclose(out); }
^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o methylKit.dll tmp.def RcppExports.o methCall.o -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/usrlib/x64 -lhts -lz -lm -lws2_32 -lpthread -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/methylKit.buildbin-libdir/methylKit/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'methylKit' as methylKit_1.6.3.zip
* DONE (methylKit)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'methylKit' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
methylKit.Rcheck/tests_i386/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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.
> library(testthat)
> library(methylKit)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
>
>
>
> test_check("methylKit")
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.unsorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.unsorted.min.sam
paired sam.
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.unsorted_chr.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.unsorted_chr.min.sam
paired sam.
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.bismark_single_end.sorted.bam
using htslib.
Conversion Statistics:
total otherC considered (>95% C+T): 20
average conversion rate = 95.184207585947
total otherC considered (Forward) (>95% C+T): 8
average conversion rate (Forward) = 97.528594771242
total otherC considered (Reverse) (>95% C+T): 12
average conversion rate (Reverse) = 93.62128279575
Done.
Reading methylation percentage per base for sample: test1
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/ctrl.bismark_paired_end.sorted.bam
using htslib.
Conversion Statistics:
total otherC considered (>95% C+T): 4
average conversion rate = 100
total otherC considered (Forward) (>95% C+T): 4
average conversion rate (Forward) = 100
total otherC considered (Reverse) (>95% C+T): 0
average conversion rate (Reverse) = 0
Done.
Reading methylation percentage per base for sample: ctrl1
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
paired sam.
Conversion Statistics:
total otherC considered (>95% C+T): 10
average conversion rate = 100
total otherC considered (Forward) (>95% C+T): 10
average conversion rate (Forward) = 100
total otherC considered (Reverse) (>95% C+T): 0
average conversion rate (Reverse) = 0
Done.
Reading methylation percentage per base for sample: test1
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
paired sam.
Conversion Statistics:
total otherC considered (>95% C+T): 10
average conversion rate = 100
total otherC considered (Forward) (>95% C+T): 10
average conversion rate (Forward) = 100
total otherC considered (Reverse) (>95% C+T): 0
average conversion rate (Reverse) = 0
Done.
Reading methylation percentage per base for sample: test1
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
paired sam.
Conversion Statistics:
total otherC considered (>95% C+T): 10
average conversion rate = 100
total otherC considered (Forward) (>95% C+T): 10
average conversion rate (Forward) = 100
total otherC considered (Reverse) (>95% C+T): 0
average conversion rate (Reverse) = 0
Done.
Reading methylation percentage per base for sample: test1
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
paired sam.
Conversion Statistics:
total otherC considered (>95% C+T): 10
average conversion rate = 100
total otherC considered (Forward) (>95% C+T): 10
average conversion rate (Forward) = 100
total otherC considered (Reverse) (>95% C+T): 0
average conversion rate (Reverse) = 0
Done.
Reading methylation percentage per base for sample: test1
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
paired sam.
Conversion Statistics:
total otherC considered (>95% C+T): 10
average conversion rate = 100
total otherC considered (Forward) (>95% C+T): 10
average conversion rate (Forward) = 100
total otherC considered (Reverse) (>95% C+T): 0
average conversion rate (Reverse) = 0
Done.
Reading methylation percentage per base for sample: test1
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
paired sam.
Conversion Statistics:
total otherC considered (>95% C+T): 10
average conversion rate = 100
total otherC considered (Forward) (>95% C+T): 10
average conversion rate (Forward) = 100
total otherC considered (Reverse) (>95% C+T): 0
average conversion rate (Reverse) = 0
Done.
Reading methylation percentage per base for sample: test1
Using internal DSS code...
Using internal DSS code...
== testthat results ===========================================================
OK: 423 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
34.32 1.39 35.67
|
methylKit.Rcheck/tests_x64/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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.
> library(testthat)
> library(methylKit)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
>
>
>
> test_check("methylKit")
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.unsorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.unsorted.min.sam
paired sam.
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.unsorted_chr.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.unsorted_chr.min.sam
paired sam.
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.bismark_single_end.sorted.bam
using htslib.
Conversion Statistics:
total otherC considered (>95% C+T): 20
average conversion rate = 95.184207585947
total otherC considered (Forward) (>95% C+T): 8
average conversion rate (Forward) = 97.528594771242
total otherC considered (Reverse) (>95% C+T): 12
average conversion rate (Reverse) = 93.62128279575
Done.
Reading methylation percentage per base for sample: test1
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/ctrl.bismark_paired_end.sorted.bam
using htslib.
Conversion Statistics:
total otherC considered (>95% C+T): 4
average conversion rate = 100
total otherC considered (Forward) (>95% C+T): 4
average conversion rate (Forward) = 100
total otherC considered (Reverse) (>95% C+T): 0
average conversion rate (Reverse) = 0
Done.
Reading methylation percentage per base for sample: ctrl1
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
paired sam.
Conversion Statistics:
total otherC considered (>95% C+T): 10
average conversion rate = 100
total otherC considered (Forward) (>95% C+T): 10
average conversion rate (Forward) = 100
total otherC considered (Reverse) (>95% C+T): 0
average conversion rate (Reverse) = 0
Done.
Reading methylation percentage per base for sample: test1
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
paired sam.
Conversion Statistics:
total otherC considered (>95% C+T): 10
average conversion rate = 100
total otherC considered (Forward) (>95% C+T): 10
average conversion rate (Forward) = 100
total otherC considered (Reverse) (>95% C+T): 0
average conversion rate (Reverse) = 0
Done.
Reading methylation percentage per base for sample: test1
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
paired sam.
Conversion Statistics:
total otherC considered (>95% C+T): 10
average conversion rate = 100
total otherC considered (Forward) (>95% C+T): 10
average conversion rate (Forward) = 100
total otherC considered (Reverse) (>95% C+T): 0
average conversion rate (Reverse) = 0
Done.
Reading methylation percentage per base for sample: test1
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
paired sam.
Conversion Statistics:
total otherC considered (>95% C+T): 10
average conversion rate = 100
total otherC considered (Forward) (>95% C+T): 10
average conversion rate (Forward) = 100
total otherC considered (Reverse) (>95% C+T): 0
average conversion rate (Reverse) = 0
Done.
Reading methylation percentage per base for sample: test1
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
paired sam.
Conversion Statistics:
total otherC considered (>95% C+T): 10
average conversion rate = 100
total otherC considered (Forward) (>95% C+T): 10
average conversion rate (Forward) = 100
total otherC considered (Reverse) (>95% C+T): 0
average conversion rate (Reverse) = 0
Done.
Reading methylation percentage per base for sample: test1
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
using htslib.
Failed to read header, falling back.
Trying to process:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
paired sam.
Conversion Statistics:
total otherC considered (>95% C+T): 10
average conversion rate = 100
total otherC considered (Forward) (>95% C+T): 10
average conversion rate (Forward) = 100
total otherC considered (Reverse) (>95% C+T): 0
average conversion rate (Reverse) = 0
Done.
Reading methylation percentage per base for sample: test1
Using internal DSS code...
Using internal DSS code...
== testthat results ===========================================================
OK: 423 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
46.48 1.10 47.95
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methylKit.Rcheck/examples_i386/methylKit-Ex.timings
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methylKit.Rcheck/examples_x64/methylKit-Ex.timings
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