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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PING.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PING_2.27.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/PING.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.27.0’
* 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 ... WARNING
Found the following significant warnings:
ping.c:321:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
ping.c:329:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
ping.c:345:12: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
ping.c:353:12: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Users/biocbuild/bbs-3.9-bioc/meat/PING.Rcheck/00install.out’ for details.
* 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 ... NOTE
Warning: no function found corresponding to methods exports from 'PING' for: 'density'
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... 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: 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 : <anonymous>: warning in symbols(x@estimates$mu +
shift * se(x), rep(0.5, K), rec = matrix(rep(c(147, 0.8), K), ncol =
2, byrow = TRUE), inches = FALSE, bg = 0, fg = grey(abs(shift) *
se(x)/(3 * (se(x)))), add = TRUE, xlim = c(m, M), ylim = c(0, 1), lwd
= 2): partial argument match of 'rec' to 'rectangles'
plot,ping-segReads: warning in symbols(x@estimates$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'
FilterPING: no visible global function definition for 'density'
NucleosomeTrack: no visible global function definition for 'as'
PostDelta: no visible global function definition for 'as'
PostDup: no visible global function definition for 'as'
PostError: no visible global function definition for 'as'
PostSigma: no visible global function definition for 'as'
RawReadsTrack: no visible global function definition for 'seqnames'
RawReadsTrack: no visible global function definition for 'strand'
make.thickthin: no visible global function definition for 'as.roman'
newPing: no visible global function definition for 'new'
newPingError: no visible global function definition for 'new'
newPingList: no visible global function definition for 'new'
postPING: no visible global function definition for 'as'
segmentPING: no visible global function definition for 'seqlevels'
truncateResult: no visible global function definition for 'read.table'
as.data.frame,pingList: no visible global function definition for 'as'
plot,data.frame-data.frame: no visible global function definition for
'pingFDR2'
plot,ping-segReads: no visible global function definition for 'density'
plot,pingError-segReads: no visible global function definition for
'density'
plot,pingList-pingList: no visible global function definition for
'pingFDR'
show,pingList: no visible global function definition for 'getSlots'
Undefined global functions or variables:
as as.roman density getSlots new pingFDR pingFDR2 read.table
seqlevels seqnames strand
Consider adding
importFrom("methods", "as", "getSlots", "new")
importFrom("stats", "density")
importFrom("utils", "as.roman", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 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 sizes of PDF files under ‘inst/doc’ ... 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, 5 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/PING.Rcheck/00check.log’
for details.
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL PING
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* 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 -fPIC -Wall -g -O2 -c init.c -o init.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c ping.c -o ping.o
ping.c:321:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
if(abs(REAL(yF)[i]-mu[k]+delta[k]/2.)/sqrt(sF[k])<calpha)
^
ping.c:321:10: note: use function 'fabs' instead
if(abs(REAL(yF)[i]-mu[k]+delta[k]/2.)/sqrt(sF[k])<calpha)
^˜˜
fabs
ping.c:329:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
if(abs(REAL(yR)[i]-mu[k]-delta[k]/2.)/sqrt(sR[k])<calpha)
^
ping.c:329:10: note: use function 'fabs' instead
if(abs(REAL(yR)[i]-mu[k]-delta[k]/2.)/sqrt(sR[k])<calpha)
^˜˜
fabs
ping.c:345:12: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
if(abs(REAL(cF)[i]-mu[k]+delta[k]/2.)/sqrt(sF[k])<calpha)
^
ping.c:345:12: note: use function 'fabs' instead
if(abs(REAL(cF)[i]-mu[k]+delta[k]/2.)/sqrt(sF[k])<calpha)
^˜˜
fabs
ping.c:353:12: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
if(abs(REAL(cR)[i]-mu[k]-delta[k]/2.)/sqrt(sR[k])<calpha)
^
ping.c:353:12: note: use function 'fabs' instead
if(abs(REAL(cR)[i]-mu[k]-delta[k]/2.)/sqrt(sR[k])<calpha)
^˜˜
fabs
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:1536:29: 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:1536:47: warning: unused variable 'aaR' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1536:52: warning: unused variable 'ggF' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
ping.c:1536:57: 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: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:1743:52: 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:1743:42: warning: unused variable 'aaF' [-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:1743:29: warning: unused variable 'etaDiff' [-Wunused-variable]
double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
^
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:2590:73: 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: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:3040:59: warning: unused variable 'PhiFRw' [-Wunused-variable]
double aNormF, aNormR, bNormF, bNormR, P0FR=1.0, PhiFR, PhiFRw, wPjFR;
^
ping.c:3301:11: warning: unused variable 'j' [-Wunused-variable]
int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
^
ping.c:3301:7: warning: unused variable 'i' [-Wunused-variable]
int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
^
28 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 /Library/Frameworks/R.framework/Versions/3.6/Resources/library/PING/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 (PING)
