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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:PICS.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings PICS_2.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/PICS.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PICS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PICS’ version ‘2.24.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘PICS’ can be installed ... WARNING
Found the following significant warnings:
pics.c:803:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
pics.c:963:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
segment.c:123:19: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
segment.c:1543:21: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
segment.c:1544:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
segment.c:1545:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
segment.c:1546:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
segment.c:1547:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
segment.c:1548:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
segment.c:1549:20: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/biocbuild/bbs-3.7-bioc/meat/PICS.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
* 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 shell scripts ... 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 ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 2 WARNINGs, 2 NOTEs
See
‘/home/biocbuild/bbs-3.7-bioc/meat/PICS.Rcheck/00check.log’
for details.
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL PICS
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘PICS’ ...
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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;
^
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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;
^
gcc -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o PICS.so pics.o segment.o -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/PICS/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (PICS)
