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BioC 3.0: CHECK report for PICS on oaxaca

This page was generated on 2015-04-10 10:04:09 -0700 (Fri, 10 Apr 2015).

Package 662/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PICS 2.10.0
Renan Sauteraud
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/PICS
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: PICS
Version: 2.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PICS_2.10.0.tar.gz
StartedAt: 2015-04-10 02:10:00 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 02:13:10 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 189.1 seconds
RetCode: 0
Status:  OK 
CheckDir: PICS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PICS_2.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/PICS.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘2.10.0’
* 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 ... [20s/22s] 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
* 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
bam2gr: no visible global function definition for ‘elementMetadata’
bam2gr: no visible global function definition for ‘elementMetadata<-’
cand_recursive: no visible global function definition for ‘width’
cand_recursive: no visible global function definition for ‘disjoin’
candidate.region: no visible global function definition for ‘viewMaxs’
candidate.region: no visible global function definition for ‘width’
candidate.region: no visible global function definition for
  ‘findOverlaps’
makeRangedDataOutput: no visible global function definition for
  ‘findOverlaps’
s_cut: no visible global function definition for ‘findOverlaps’
s_cut: no visible global function definition for ‘viewMins’
segChrRead: no visible global function definition for ‘findOverlaps’
segChrRead: no visible global function definition for ‘start<-’
segChrRead: no visible global function definition for ‘end<-’
* 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 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 ... [11s/11s] 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/PICS.Rcheck/00check.log’
for details.

PICS.Rcheck/00install.out:

* installing *source* package ‘PICS’ ...
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 pics.c -o pics.o
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: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: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:1009:66: 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: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: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:1301:3: warning: variable 'penalty' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
                default:
                ^˜˜˜˜˜˜
pics.c:1307:97: note: uninitialized use occurs here
        bic = logDensityMix(yF, w, muF, sigmaSqF, K, NF) + logDensityMix(yR, w, muR, sigmaSqR, K,NR) - penalty;
                                                                                                       ^˜˜˜˜˜˜
pics.c:1275:42: note: initialize the variable 'penalty' to silence this warning
        double bic, tmp, muF[K], muR[K], penalty, distance;
                                                ^
                                                 = 0.0
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: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:1889:7: warning: unused variable 'i' [-Wunused-variable]
  int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
      ^
pics.c:1889:11: warning: unused variable 'j' [-Wunused-variable]
  int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
          ^
15 warnings generated.
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 segment.c -o segment.o
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:308:7: warning: unused variable 'i' [-Wunused-variable]
  int i=0,p=0;
      ^
segment.c:1364:11: warning: unused variable 'j' [-Wunused-variable]
        int i=0, j=0, n=length(list), nF, nR, nProtect=0;
                 ^
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;
          ^
5 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 PICS.so pics.o segment.o -L/usr/local/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/PICS.Rcheck/PICS/libs
** R
** inst
** preparing package for lazy loading
No methods found in "IRanges" for requests: levels, as.factor, elementMetadata, elementMetadata<-
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "IRanges" for requests: levels, as.factor, elementMetadata, elementMetadata<-
* DONE (PICS)

PICS.Rcheck/PICS-Ex.timings:

nameusersystemelapsed
makeRangedDataOutput0.0000.0000.001
pics-class0.0020.0010.002
picsError-class0.0030.0000.003
picsList-class0.0030.0000.003
segmentPICS2.2120.0442.260
setParaPrior0.0010.0000.001