Back to Multiple platform build/check report for BioC 3.9
ABCDEFGHIJKLMN[O]PQRSTUVWXYZ

INSTALL report for openCyto on malbec2

This page was generated on 2019-10-16 12:03:30 -0400 (Wed, 16 Oct 2019).

Package 1143/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
openCyto 1.22.2
Mike Jiang
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/openCyto
Branch: RELEASE_3_9
Last Commit: 230adb5
Last Changed Date: 2019-06-03 16:55:58 -0400 (Mon, 03 Jun 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64 [ OK ] OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: openCyto
Version: 1.22.2
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL openCyto
StartedAt: 2019-10-15 18:54:52 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 18:56:21 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 88.9 seconds
RetCode: 0
Status:  OK 

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL openCyto
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘openCyto’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c cpPmden.cpp -o cpPmden.o
cpPmden.cpp: In function ‘stringInfo cpPmden(const std::vector&)’:
cpPmden.cpp:88:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (auto i = 0; i < (nsamp-1); i++) {
                    ~~^~~~~~~~~~~
cpPmden.cpp:100:17: warning: variable ‘newaccx’ set but not used [-Wunused-but-set-variable]
     double rhs, newaccx;
                 ^~~~~~~
cpPmden.cpp:156:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (auto i = 0; i < nsamp; i++) {
                      ~~^~~~~~~
cpPmden.cpp:162:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (auto i=0; i < (nsamp-2); i++) {
                    ~~^~~~~~~~~~~
cpPmden.cpp:186:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (auto i = 0; i < nsamp; i++) {
                      ~~^~~~~~~
cpPmden.cpp:212:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (auto i = 0; i < nsamp; i++) {
                        ~~^~~~~~~
cpPmden.cpp:244:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (auto i = 0; i < nsamp; i++) {
                        ~~^~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c cppApprox.cpp -o cppApprox.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c cppdip.cpp -o cppdip.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c dynamic_prog.cpp -o dynamic_prog.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c fill_SMAWK.cpp -o fill_SMAWK.o
fill_SMAWK.cpp: In function ‘void reduce_in_place(int, int, int, int, const std::vector&, std::vector&, const std::vector >&, const std::vector >&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, DISSIMILARITY)’:
fill_SMAWK.cpp:80:8: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(N >= js.size()) {
      ~~^~~~~~~~~~~~
fill_SMAWK.cpp:90:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   while(m > N) { // js_reduced has more than N positions / columns
         ~~^~~
fill_SMAWK.cpp:121:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int r=(left+1); r < m; ++r) {
                       ~~^~~
fill_SMAWK.cpp: In function ‘void fill_even_positions(int, int, int, int, const std::vector&, std::vector >&, std::vector >&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, DISSIMILARITY)’:
fill_SMAWK.cpp:164:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(++ r; r < n && js[r]<=jmax; r++) {
               ~~^~~
fill_SMAWK.cpp:164:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(++ r; r < n && js[r]<=jmax; r++) {
fill_SMAWK.cpp:168:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if(jabs > i) break;
          ~~~~~^~~
fill_SMAWK.cpp: In function ‘void find_min_from_candidates(int, int, int, int, const std::vector&, std::vector >&, std::vector >&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, DISSIMILARITY)’:
fill_SMAWK.cpp:218:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if(j_abs > i) break;
          ~~~~~~^~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c getTautStringApprox.cpp -o getTautStringApprox.o
getTautStringApprox.cpp: In function ‘Rcpp::List getTautStringApprox(std::vector)’:
getTautStringApprox.cpp:32:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i = 1; i != fullString.size(); ++i) {
                   ~~^~~~~~~~~~~~~~~~~~~~
getTautStringApprox.cpp:56:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i  = 0; i != plotSpecs.size(); ++i) {
                    ~~^~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c kMedDP.cpp -o kMedDP.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c kkuiper.cpp -o kkuiper.o
kkuiper.cpp: In function ‘void difficultmax(std::vector&, long int, long int, long int, long int*, long int*, double*)’:
kkuiper.cpp:77:10: warning: variable ‘min’ set but not used [-Wunused-but-set-variable]
   double min, max;
          ^~~
kkuiper.cpp: In function ‘void easymax(std::vector&, long int, long int, long int, long int*, long int*, double*)’:
kkuiper.cpp:64:10: warning: ‘maxi’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     *erga=maxi;
     ~~~~~^~~~~
kkuiper.cpp:63:10: warning: ‘mini’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     *ergb=mini;
     ~~~~~^~~~~
kkuiper.cpp: In function ‘void difficultmax(std::vector&, long int, long int, long int, long int*, long int*, double*)’:
kkuiper.cpp:161:23: warning: ‘maxi’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       *erga=minis[maxi];
                       ^
kkuiper.cpp: In function ‘std::vector kkuiper(std::vector&, long int, int)’:
kkuiper.cpp:176:15: warning: ‘maxi’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   long i,mini,maxi,maxa,maxb,newa,newb,einordnen ;
               ^~~~
kkuiper.cpp:176:10: warning: ‘mini’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   long i,mini,maxi,maxa,maxb,newa,newb,einordnen ;
          ^~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c local_density.cpp -o local_density.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c medianAbsoluteDeviation.cpp -o medianAbsoluteDeviation.o
medianAbsoluteDeviation.cpp: In function ‘double medianAbsoluteDeviation(const std::vector&)’:
medianAbsoluteDeviation.cpp:28:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (auto i = 0; i != devs.size(); ++i)
                    ~~^~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c misc.cpp -o misc.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c rQuantile.cpp -o rQuantile.o
rQuantile.cpp: In function ‘std::vector rQuantile(const std::vector&, std::vector)’:
rQuantile.cpp:35:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (auto i = 0; i != lowInd.size(); ++i) {
                    ~~^~~~~~~~~~~~~~~~
rQuantile.cpp:41:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (auto i = 0; i != lowInd.size(); ++i) {
                    ~~^~~~~~~~~~~~~~~~
rQuantile.cpp:47:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (auto i = 0; i != offSet.size(); ++i)
                    ~~^~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c singleDip.cpp -o singleDip.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c tautstring.cpp -o tautstring.o
tautstring.cpp: In function ‘stringInfo tautString(const std::vector&, const std::vector&, const std::vector&, const std::vector&, double, double, long int, int)’:
tautstring.cpp:148:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (auto i = 0; i < knotst.size(); i++) {
                    ~~^~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c tsGates.cpp -o tsGates.o
tsGates.cpp: In function ‘std::vector findKmedGates(const std::vector&, const std::vector&, int)’:
tsGates.cpp:41:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (auto j = 0; j != classVector.size(); j++)
                      ~~^~~~~~~~~~~~~~~~~~~~~
tsGates.cpp: In function ‘std::vector tsGates(const std::vector&, int)’:
tsGates.cpp:81:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (auto i = 1; i != (localMins.size()-1); ++i) {
                      ~~^~~~~~~~~~~~~~~~~~~~~~~
tsGates.cpp:86:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (auto i = 0; i != yvals.size(); ++i)
                      ~~^~~~~~~~~~~~~~~
tsGates.cpp:96:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (auto j = 0; j != cutValues.size(); ++j) {
                      ~~^~~~~~~~~~~~~~~~~~~
tsGates.cpp:99:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (auto i = 0; i != ys.size(); ++i)
                        ~~^~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c unlockNamespace.c -o unlockNamespace.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o openCyto.so RcppExports.o cpPmden.o cppApprox.o cppdip.o dynamic_prog.o fill_SMAWK.o getTautStringApprox.o kMedDP.o kkuiper.o local_density.o medianAbsoluteDeviation.o misc.o rQuantile.o singleDip.o tautstring.o tsGates.o unlockNamespace.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-openCyto/00new/openCyto/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (openCyto)