##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf PICS.buildbin-libdir PICS.Rcheck && mkdir PICS.buildbin-libdir PICS.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PICS.buildbin-libdir PICS_2.20.0.tar.gz >PICS.Rcheck\00install.out 2>&1 && cp PICS.Rcheck\00install.out PICS-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=PICS.buildbin-libdir --install="check:PICS-install.out" --force-multiarch --no-vignettes --timings PICS_2.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/PICS.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PICS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PICS' version '2.20.0'
* 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 'PICS' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* 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
':::' calls which should be '::':
'parallel:::detectCores' 'parallel:::makeCluster'
'parallel:::parLapply' 'parallel:::stopCluster'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plot,pics-segReads: warning in symbols((map[, 1] + map[, 2])/2,
rep(0.35, nMap), rectangle = cbind(map[, 2] - map[, 1], rep(0.6,
nMap)), inches = FALSE, bg = grey(0.6), fg = 0, add = TRUE, xlim =
c(m, M), ylim = c(0, 1)): partial argument match of 'rectangle' to
'rectangles'
plot,pics-segReads: warning in symbols(x@estimates$mu, rep(0.5, K), rec
= matrix(rep(c(147, 0.8), K), ncol = 2, byrow = TRUE), inches =
FALSE, bg = grey(0.5 * pmin(se(x)/50, 1)), fg = 0, add = TRUE, xlim =
c(m, M), ylim = c(0, 1)): partial argument match of 'rec' to
'rectangles'
plot,pics-segReads: warning in symbols(x@estimates$mu, rep(0.5, K), rec
= matrix(rep(c(147, 0.8), K), ncol = 2, byrow = TRUE), inches =
FALSE, fg = 0, bg = 1, add = TRUE, xlim = c(m, M), ylim = c(0, 1)):
partial argument match of 'rec' to 'rectangles'
bam2gr: no visible global function definition for 'reshape'
Undefined global functions or variables:
reshape
Consider adding
importFrom("stats", "reshape")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'picsList,ANY,ANY,ANY'
generic '[' and siglist 'segReadsList,ANY,ANY,ANY'
generic '[' and siglist 'segReadsListPE,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both 'src/Makevars.in' and 'src/Makevars'.
Installation with --no-configure' is unlikely to work. If you intended
'src/Makevars' to be used on Windows, rename it to 'src/Makevars.win'
otherwise remove it. If 'configure' created 'src/Makevars', you need a
'cleanup' script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.5-bioc/meat/PICS.buildbin-libdir/PICS/libs/i386/PICS.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
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
** running examples for arch 'x64' ... 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, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/PICS.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'PICS' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c pics.c -o pics.o
pics.c: In function 'iterEM':
pics.c:581:25: warning: unused variable 'mu' [-Wunused-variable]
double oldMu[p], w[p], mu[p], delta[p], sF[p], sR[p], sumDiff=0;
^
pics.c: In function 'ECM1':
pics.c:803:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(status1==0 & status2==0)
^
pics.c:963:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(status1==0 & status2==0)
^
pics.c:651:15: warning: unused variable 'k' [-Wunused-variable]
int i=0,j=0, k=0, K=length(VECTOR_ELT(para, 0)), NF=length(F), NR=length(R);
^
pics.c: In function 'ECM2':
pics.c:1009:66: warning: unused variable 'ee' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
pics.c:1009:57: warning: unused variable 'ggR' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
pics.c:1009:52: warning: unused variable 'ggF' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
pics.c:1009:47: warning: unused variable 'aaR' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
pics.c:1009:42: warning: unused variable 'aaF' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
pics.c:1009:29: warning: unused variable 'etaDiff' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
pics.c:1009:9: warning: variable 'chiSum' set but not used [-Wunused-but-set-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
pics.c:1000:15: warning: unused variable 'k' [-Wunused-variable]
int i=0,j=0, k=0, K=length(VECTOR_ELT(para, 0)), NF=length(F), NR=length(R);
^
pics.c: In function 'BIC':
pics.c:1272:96: warning: unused variable 'k' [-Wunused-variable]
int nu=INTEGER(nuC)[0], K=length(VECTOR_ELT(para, 0)), NF=length(F), NR=length(R), i=0, j=0, k=0, N, type=INTEGER(mselect)[0];
^
pics.c: In function 'getInfMat':
pics.c:1633:76: warning: unused variable 'PhiRw' [-Wunused-variable]
double aNormF, aNormR, bNormF, bNormR, P0F=1, P0R=1, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR;
^
pics.c:1633:69: warning: unused variable 'PhiFw' [-Wunused-variable]
double aNormF, aNormR, bNormF, bNormR, P0F=1, P0R=1, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR;
^
pics.c: In function 'mergePeak':
pics.c:1889:11: warning: unused variable 'j' [-Wunused-variable]
int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
^
pics.c:1889:7: warning: unused variable 'i' [-Wunused-variable]
int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
^
pics.c: In function 'BIC':
pics.c:1307:6: warning: 'penalty' may be used uninitialized in this function [-Wmaybe-uninitialized]
bic = logDensityMix(yF, w, muF, sigmaSqF, K, NF) + logDensityMix(yR, w, muR, sigmaSqR, K,NR) - penalty;
^
pics.c: In function 'fitModelK':
pics.c:421:18: warning: 'firstFit' may be used uninitialized in this function [-Wmaybe-uninitialized]
SEXP ans, temp, firstFit;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c segment.c -o segment.o
segment.c: In function 'segReads':
segment.c:123:19: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(length(contF)>0 & length(contR)>0)
^
segment.c:114:45: warning: unused variable 'count' [-Wunused-variable]
int i=0,nR=length(dataR),nF=length(dataF),count=0,lengthCenter=0;
^
segment.c: In function 'callRegions':
segment.c:308:7: warning: unused variable 'i' [-Wunused-variable]
int i=0,p=0;
^
segment.c: In function 'getSegL':
segment.c:1364:11: warning: unused variable 'j' [-Wunused-variable]
int i=0, j=0, n=length(list), nF, nR, nProtect=0;
^
segment.c: In function 'getDensity':
segment.c:1543:21: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if((delta[k]>deltaFilter[0] & delta[k]<deltaFilter[1]) &
^
segment.c:1544:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
(sF[k]>sFFilter[0] & sF[k]<sFFilter[1]) &
^
segment.c:1545:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
(sR[k]>sRFilter[0] & sR[k]<sRFilter[1]) &
^
segment.c:1546:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
(se[k]>seFilter[0] & se[k]<seFilter[1]) &
^
segment.c:1547:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
(se[k]>seFilterF[0] & se[k]<seFilterF[1]) &
^
segment.c:1548:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
(se[k]>seFilterR[0] & se[k]<seFilterR[1]) &
^
segment.c:1549:20: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
(score[k]>scoreFilter[0] & score[k]<scoreFilter[1]))
^
segment.c:1494:19: warning: variable 'chr' set but not used [-Wunused-but-set-variable]
SEXP ans, x, y, chr, names;
^
segment.c:1490:8: warning: unused variable 'filter1' [-Wunused-variable]
SEXP filter1;
^
segment.c:1489:11: warning: unused variable 'muFilter' [-Wunused-variable]
double *muFilter, *deltaFilter, *sFFilter, *sRFilter, *seFilter, *seFilterF, *seFilterR, *scoreFilter, *score;
^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o PICS.dll tmp.def pics.o segment.o -lws2_32 -L/i386/lib -lgsl -lgslcblas -lm -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/PICS.buildbin-libdir/PICS/libs/i386
** R
** 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 'PICS' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c pics.c -o pics.o
pics.c: In function 'iterEM':
pics.c:581:25: warning: unused variable 'mu' [-Wunused-variable]
double oldMu[p], w[p], mu[p], delta[p], sF[p], sR[p], sumDiff=0;
^
pics.c: In function 'ECM1':
pics.c:803:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(status1==0 & status2==0)
^
pics.c:963:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(status1==0 & status2==0)
^
pics.c:651:15: warning: unused variable 'k' [-Wunused-variable]
int i=0,j=0, k=0, K=length(VECTOR_ELT(para, 0)), NF=length(F), NR=length(R);
^
pics.c: In function 'ECM2':
pics.c:1009:66: warning: unused variable 'ee' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
pics.c:1009:57: warning: unused variable 'ggR' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
pics.c:1009:52: warning: unused variable 'ggF' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
pics.c:1009:47: warning: unused variable 'aaR' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
pics.c:1009:42: warning: unused variable 'aaF' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
pics.c:1009:29: warning: unused variable 'etaDiff' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
pics.c:1009:9: warning: variable 'chiSum' set but not used [-Wunused-but-set-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
pics.c:1000:15: warning: unused variable 'k' [-Wunused-variable]
int i=0,j=0, k=0, K=length(VECTOR_ELT(para, 0)), NF=length(F), NR=length(R);
^
pics.c: In function 'BIC':
pics.c:1272:96: warning: unused variable 'k' [-Wunused-variable]
int nu=INTEGER(nuC)[0], K=length(VECTOR_ELT(para, 0)), NF=length(F), NR=length(R), i=0, j=0, k=0, N, type=INTEGER(mselect)[0];
^
pics.c: In function 'getInfMat':
pics.c:1633:76: warning: unused variable 'PhiRw' [-Wunused-variable]
double aNormF, aNormR, bNormF, bNormR, P0F=1, P0R=1, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR;
^
pics.c:1633:69: warning: unused variable 'PhiFw' [-Wunused-variable]
double aNormF, aNormR, bNormF, bNormR, P0F=1, P0R=1, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR;
^
pics.c: In function 'mergePeak':
pics.c:1889:11: warning: unused variable 'j' [-Wunused-variable]
int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
^
pics.c:1889:7: warning: unused variable 'i' [-Wunused-variable]
int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
^
pics.c: In function 'BIC':
pics.c:1307:6: warning: 'penalty' may be used uninitialized in this function [-Wmaybe-uninitialized]
bic = logDensityMix(yF, w, muF, sigmaSqF, K, NF) + logDensityMix(yR, w, muR, sigmaSqR, K,NR) - penalty;
^
pics.c: In function 'fitModelK':
pics.c:421:18: warning: 'firstFit' may be used uninitialized in this function [-Wmaybe-uninitialized]
SEXP ans, temp, firstFit;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c segment.c -o segment.o
segment.c: In function 'segReads':
segment.c:123:19: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(length(contF)>0 & length(contR)>0)
^
segment.c:114:45: warning: unused variable 'count' [-Wunused-variable]
int i=0,nR=length(dataR),nF=length(dataF),count=0,lengthCenter=0;
^
segment.c: In function 'callRegions':
segment.c:308:7: warning: unused variable 'i' [-Wunused-variable]
int i=0,p=0;
^
segment.c: In function 'getSegL':
segment.c:1364:11: warning: unused variable 'j' [-Wunused-variable]
int i=0, j=0, n=length(list), nF, nR, nProtect=0;
^
segment.c: In function 'getDensity':
segment.c:1543:21: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if((delta[k]>deltaFilter[0] & delta[k]<deltaFilter[1]) &
^
segment.c:1544:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
(sF[k]>sFFilter[0] & sF[k]<sFFilter[1]) &
^
segment.c:1545:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
(sR[k]>sRFilter[0] & sR[k]<sRFilter[1]) &
^
segment.c:1546:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
(se[k]>seFilter[0] & se[k]<seFilter[1]) &
^
segment.c:1547:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
(se[k]>seFilterF[0] & se[k]<seFilterF[1]) &
^
segment.c:1548:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
(se[k]>seFilterR[0] & se[k]<seFilterR[1]) &
^
segment.c:1549:20: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
(score[k]>scoreFilter[0] & score[k]<scoreFilter[1]))
^
segment.c:1494:19: warning: variable 'chr' set but not used [-Wunused-but-set-variable]
SEXP ans, x, y, chr, names;
^
segment.c:1490:8: warning: unused variable 'filter1' [-Wunused-variable]
SEXP filter1;
^
segment.c:1489:11: warning: unused variable 'muFilter' [-Wunused-variable]
double *muFilter, *deltaFilter, *sFFilter, *sRFilter, *seFilter, *seFilterF, *seFilterR, *scoreFilter, *score;
^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o PICS.dll tmp.def pics.o segment.o -lws2_32 -L/x64/lib -lgsl -lgslcblas -lm -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/PICS.buildbin-libdir/PICS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PICS' as PICS_2.20.0.zip
* DONE (PICS)
