BioC 3.4: CHECK report for methylKit on tokay1

Package: methylKit

Version: 1.0.0

Command: rm -rf methylKit.buildbin-libdir methylKit.Rcheck && mkdir methylKit.buildbin-libdir methylKit.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=methylKit.buildbin-libdir methylKit_1.0.0.tar.gz >methylKit.Rcheck\00install.out 2>&1 && cp methylKit.Rcheck\00install.out methylKit-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=methylKit.buildbin-libdir --install="check:methylKit-install.out" --force-multiarch --no-vignettes --timings methylKit_1.0.0.tar.gz

StartedAt: 2017-04-14 23:29:03 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:35:58 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 415.3 seconds

RetCode: 0

Status:  OK

CheckDir: methylKit.Rcheck

Warnings: 0

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###
### Running command:
###
###   rm -rf methylKit.buildbin-libdir methylKit.Rcheck && mkdir methylKit.buildbin-libdir methylKit.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=methylKit.buildbin-libdir methylKit_1.0.0.tar.gz >methylKit.Rcheck\00install.out 2>&1 && cp methylKit.Rcheck\00install.out methylKit-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=methylKit.buildbin-libdir --install="check:methylKit-install.out" --force-multiarch --no-vignettes --timings methylKit_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/methylKit.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.0.0'
* 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 'methylKit' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   2.5Mb
* 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 ... 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-3.4-bioc/meat/methylKit.buildbin-libdir/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)
  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
calculateDiffMeth-methods 6.79   0.04    6.85
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
calculateDiffMeth-methods 7.93   0.11    8.03
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/methylKit.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'methylKit' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c methCall.cpp -o methCall.o
methCall.cpp: In function 'void processCigar(std::string, std::string&, std::string&)':
methCall.cpp:492:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=0;i < insPos.size();i++){
                   ^
methCall.cpp: In function 'int process_sam(std::istream*, std::string&, std::string&, std::string&, int&, int&, int&, int, int)':
methCall.cpp:633:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for( int i=0; i < quals.length(); i++) 
                     ^
methCall.cpp: In function 'int process_bam(std::string&, std::string&, std::string&, std::string&, int&, int&, int&, int)':
methCall.cpp:809:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 1; i < len_cigar; i++  ) {
                   ^
methCall.cpp:898:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for( int i=0; i < quals.length(); i++) 
                     ^
methCall.cpp: In function 'int process_single_bismark(std::istream*, std::string&, std::string&, std::string&, int&, int&, int&)':
methCall.cpp:1075:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for( int i=0; i < quals.length(); i++) 
                     ^
methCall.cpp:1079:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if( ( (gbases[i] == 'C') && (i==quals.length()) ) && ( gbases.substr(i-1,4) == "CCGG" ) ) { continue;} 
                                     ^
methCall.cpp: In function 'int process_sam(std::istream*, std::string&, std::string&, std::string&, int&, int&, int&, int, int)':
methCall.cpp:637:7: warning: 'strand' may be used uninitialized in this function [-Wmaybe-uninitialized]
       if( strand == '+') { key = "F|"+ chr+"|"+std::to_string(static_cast<long long>(start+i)); }
       ^
methCall.cpp:651:84: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
                                                                                    ^
methCall.cpp:650:84: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
                                                                                    ^
methCall.cpp:649:81: 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:902:7: warning: 'strand' may be used uninitialized in this function [-Wmaybe-uninitialized]
       if( strand == '+') { key = "F|"+ chr+"|"+std::to_string(static_cast<long long>(start+i)); }
       ^
methCall.cpp:916:84: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
                                                                                    ^
methCall.cpp:915:84: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
                                                                                    ^
methCall.cpp:914:81: 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:1097:84: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
                                                                                    ^
methCall.cpp:1096:84: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
                                                                                    ^
methCall.cpp:1095:81: 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-3.4-bioc/R/library/Rhtslib/lib/i386 -lhts -lz -pthread -lws2_32 -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/methylKit.buildbin-libdir/methylKit/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 'methylKit' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c methCall.cpp -o methCall.o
methCall.cpp: In function 'void processCigar(std::string, std::string&, std::string&)':
methCall.cpp:492:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=0;i < insPos.size();i++){
                   ^
methCall.cpp: In function 'int process_sam(std::istream*, std::string&, std::string&, std::string&, int&, int&, int&, int, int)':
methCall.cpp:633:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for( int i=0; i < quals.length(); i++) 
                     ^
methCall.cpp: In function 'int process_bam(std::string&, std::string&, std::string&, std::string&, int&, int&, int&, int)':
methCall.cpp:809:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 1; i < len_cigar; i++  ) {
                   ^
methCall.cpp:898:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for( int i=0; i < quals.length(); i++) 
                     ^
methCall.cpp: In function 'int process_single_bismark(std::istream*, std::string&, std::string&, std::string&, int&, int&, int&)':
methCall.cpp:1075:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for( int i=0; i < quals.length(); i++) 
                     ^
methCall.cpp:1079:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if( ( (gbases[i] == 'C') && (i==quals.length()) ) && ( gbases.substr(i-1,4) == "CCGG" ) ) { continue;} 
                                     ^
methCall.cpp: In function 'int process_sam(std::istream*, std::string&, std::string&, std::string&, int&, int&, int&, int, int)':
methCall.cpp:637:7: warning: 'strand' may be used uninitialized in this function [-Wmaybe-uninitialized]
       if( strand == '+') { key = "F|"+ chr+"|"+std::to_string(static_cast<long long>(start+i)); }
       ^
methCall.cpp:651:84: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
                                                                                    ^
methCall.cpp:650:84: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
                                                                                    ^
methCall.cpp:649:81: 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:902:7: warning: 'strand' may be used uninitialized in this function [-Wmaybe-uninitialized]
       if( strand == '+') { key = "F|"+ chr+"|"+std::to_string(static_cast<long long>(start+i)); }
       ^
methCall.cpp:916:84: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
                                                                                    ^
methCall.cpp:915:84: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
                                                                                    ^
methCall.cpp:914:81: 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:1097:84: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
                                                                                    ^
methCall.cpp:1096:84: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
                                                                                    ^
methCall.cpp:1095:81: 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-3.4-bioc/R/library/Rhtslib/lib/x64 -lhts -lz -pthread -lws2_32 -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/methylKit.buildbin-libdir/methylKit/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'methylKit' as methylKit_1.0.0.zip
* DONE (methylKit)

name	user	system	elapsed
PCASamples-methods	0.03	0.00	0.03
adjustMethylC	0.05	0.00	0.05
assocComp-methods	0.02	0.00	0.02
bedgraph-methods	0.05	0.00	0.06
calculateDiffMeth-methods	6.79	0.04	6.85
calculateDiffMethDSS-methods	0.50	0.02	0.51
clusterSamples-methods	0.02	0.00	0.02
dataSim-methods	0.06	0.00	0.06
diffMethPerChr-methods	0.02	0.00	0.01
extract-methods	0.01	0.01	0.04
filterByCoverage-methods	0.06	0.00	0.09
getAssembly-methods	0.36	0.00	0.36
getContext-methods	0	0	0
getCorrelation-methods	0.07	0.00	0.09
getCoverageStats-methods	0	0	0
getDBPath-methods	0.03	0.02	0.05
getData-methods	0.01	0.00	0.02
getMethylDiff-methods	0.02	0.00	0.01
getMethylationStats-methods	0.02	0.00	0.02
getSampleID-methods	0.00	0.01	0.01
getTreatment-methods	0.00	0.02	0.02
makeMethylDB-methods	0	0	0
methRead-methods	0.28	0.00	0.34
methSeg	0.01	0.00	0.02
methylBase-class	0.02	0.00	0.01
methylBaseDB-class	0.06	0.00	0.13
methylDiff-class	0.02	0.00	0.01
methylDiffDB-class	1.67	0.06	1.74
methylRaw-class	0.03	0.02	0.05
methylRawDB-class	0.06	0.01	0.07
methylRawList-class	0.02	0.00	0.02
methylRawListDB-class	0.15	0.00	0.16
normalizeCoverage-methods	0.16	0.00	0.15
percMethylation-methods	0	0	0
pool-methods	0.02	0.00	0.02
processBismarkAln-methods	0.04	0.00	0.04
reconstruct-methods	0.02	0.00	0.02
regionCounts	0.2	0.0	0.2
removeComp-methods	0.03	0.00	0.03
reorganize-methods	0.14	0.00	0.13
select-methods	0.08	0.00	0.08
selectByOverlap-methods	2.07	0.05	2.12
show-methods	0.01	0.00	0.02
tileMethylCounts-methods	0.39	0.02	0.41
unite-methods	0.11	0.00	0.11

name	user	system	elapsed
PCASamples-methods	0.02	0.00	0.01
adjustMethylC	0.56	0.00	0.56
assocComp-methods	0.02	0.00	0.01
bedgraph-methods	0.01	0.01	0.03
calculateDiffMeth-methods	7.93	0.11	8.03
calculateDiffMethDSS-methods	0.59	0.00	0.60
clusterSamples-methods	0.03	0.00	0.03
dataSim-methods	0.03	0.00	0.03
diffMethPerChr-methods	0.02	0.00	0.02
extract-methods	0.01	0.00	0.01
filterByCoverage-methods	0.05	0.03	0.08
getAssembly-methods	0.02	0.00	0.02
getContext-methods	0	0	0
getCorrelation-methods	0.57	0.03	0.67
getCoverageStats-methods	0	0	0
getDBPath-methods	0.05	0.00	0.05
getData-methods	0.01	0.00	0.02
getMethylDiff-methods	0.02	0.00	0.01
getMethylationStats-methods	0.01	0.02	0.03
getSampleID-methods	0	0	0
getTreatment-methods	0.02	0.00	0.02
makeMethylDB-methods	0	0	0
methRead-methods	0.27	0.02	0.28
methSeg	0	0	0
methylBase-class	0	0	0
methylBaseDB-class	0.06	0.01	0.08
methylDiff-class	0.01	0.00	0.02
methylDiffDB-class	1.88	0.00	2.01
methylRaw-class	0.05	0.00	0.05
methylRawDB-class	0.06	0.00	0.06
methylRawList-class	0.02	0.00	0.01
methylRawListDB-class	0.12	0.00	0.55
normalizeCoverage-methods	0.14	0.00	0.33
percMethylation-methods	0.00	0.01	0.02
pool-methods	0.02	0.00	0.01
processBismarkAln-methods	0.05	0.00	0.05
reconstruct-methods	0.01	0.00	0.01
regionCounts	0.22	0.00	0.22
removeComp-methods	0.03	0.00	0.03
reorganize-methods	0.09	0.00	0.09
select-methods	0.08	0.00	0.08
selectByOverlap-methods	2.19	0.02	2.20
show-methods	0.01	0.00	0.02
tileMethylCounts-methods	0.46	0.00	0.45
unite-methods	0.09	0.02	0.09