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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PING_2.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/PING.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PING/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PING’ version ‘2.14.0’
* 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 ‘PING’ can be installed ... [33s/38s] OK
* checking installed package size ... NOTE
installed size is 7.5Mb
sub-directories of 1Mb or more:
extdata 5.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘IRanges’
A package should be listed in only one of these fields.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘BSgenome’ ‘BiocGenerics’ ‘fda’ ‘methods’
All declared Imports should be used.
Packages in Depends field not imported from:
‘GenomicRanges’ ‘chipseq’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
':::' 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,ping-segReads : .local: 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,ping-segReads : .local : <anonymous>: warning in
symbols(x@estimates$mu + shift * se(x), rep(0.5, K), rec =
matrix(rep(c(147, 0.8), K), ncol = 2, byrow = TRUE), inches = FALSE,
bg = 0, fg = grey(abs(shift) * se(x)/(3 * (se(x)))), add = TRUE, xlim
= c(m, M), ylim = c(0, 1), lwd = 2): partial argument match of 'rec'
to 'rectangles'
plot,ping-segReads : .local: warning in symbols(x@estimates$mu,
rep(0.5, K), rec = matrix(rep(c(147, 0.8), K), ncol = 2, byrow =
TRUE), inches = FALSE, bg = "white", fg = grey(abs(0)), add = TRUE,
xlim = c(m, M), ylim = c(0, 1)): partial argument match of 'rec' to
'rectangles'
CoverageTrack: no visible global function definition for ‘seqnames’
RawReadsTrack: no visible global function definition for ‘seqnames’
RawReadsTrack: no visible global function definition for ‘strand’
segmentPING: no visible global function definition for ‘seqlevels’
plot,data.frame-data.frame : .local: no visible global function
definition for ‘pingFDR2’
plot,pingList-pingList : .local: no visible global function definition
for ‘pingFDR’
* 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 'pingList,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 ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [18s/18s] 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
‘/Users/biocbuild/bbs-3.2-bioc/meat/PING.Rcheck/00check.log’
for details.
* installing *source* package ‘PING’ ...
checking for pkg-config... /usr/local/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
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c init.c -o init.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c ping.c -o ping.o
ping.c:659:25: warning: unused variable 'mu' [-Wunused-variable]
double oldMu[p], w[p], mu[p], delta[p], sF[p], sR[p], sumDiff=0.0;
^
ping.c:760:15: 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);
^
ping.c:1108:15: warning: unused variable 'k' [-Wunused-variable]
int i=0,j=0, k=0, K=length(VECTOR_ELT(para, 0)), NFR=length(F);
^
ping.c:1536:52: warning: unused variable 'ggF' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1536:47: warning: unused variable 'aaR' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1536:57: warning: unused variable 'ggR' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1536:66: warning: unused variable 'ee' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1536:29: warning: unused variable 'etaDiff' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1527:15: 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);
^
ping.c:1536:42: warning: unused variable 'aaF' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1743:42: warning: unused variable 'aaF' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1743:52: warning: unused variable 'ggF' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1743:47: warning: unused variable 'aaR' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1743:66: warning: unused variable 'ee' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1743:57: warning: unused variable 'ggR' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1743:29: warning: unused variable 'etaDiff' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1734:15: warning: unused variable 'k' [-Wunused-variable]
int i=0,j=0, k=0, K=length(VECTOR_ELT(para, 0)), NFR=length(F);
^
ping.c:2095:3: warning: variable 'penalty' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
default:
^˜˜˜˜˜˜
ping.c:2101:97: note: uninitialized use occurs here
bic = logDensityMix(yF, w, muF, sigmaSqF, K, NF) + logDensityMix(yR, w, muR, sigmaSqR, K,NR) - penalty;
^˜˜˜˜˜˜
ping.c:2058:48: note: initialize the variable 'penalty' to silence this warning
double bic, tmp, tmp2, muF[K], muR[K], penalty, distance;
^
= 0.0
ping.c:2202:3: warning: variable 'penalty' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
default:
^˜˜˜˜˜˜
ping.c:2208:75: note: uninitialized use occurs here
bic = logDensityMixPE(yF, yR, w, muF, muR, sigmaSqF, sigmaSqR, K, NFR) - penalty;
^˜˜˜˜˜˜
ping.c:2165:48: note: initialize the variable 'penalty' to silence this warning
double bic, tmp, tmp2, muF[K], muR[K], penalty, distance;
^
= 0.0
ping.c:2590:80: warning: unused variable 'PhiRw' [-Wunused-variable]
double aNormF, aNormR, bNormF, bNormR, P0F=1.0, P0R=1.0, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR;
^
ping.c:2590:73: warning: unused variable 'PhiFw' [-Wunused-variable]
double aNormF, aNormR, bNormF, bNormR, P0F=1.0, P0R=1.0, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR;
^
ping.c:3040:59: warning: unused variable 'PhiFRw' [-Wunused-variable]
double aNormF, aNormR, bNormF, bNormR, P0FR=1.0, PhiFR, PhiFRw, wPjFR;
^
ping.c:3301:7: warning: unused variable 'i' [-Wunused-variable]
int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
^
ping.c:3301:11: warning: unused variable 'j' [-Wunused-variable]
int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
^
24 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o PING.so init.o ping.o -L/usr/local/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/PING.Rcheck/PING/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (PING)
