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BioC 3.4: INSTALL report for MSnbase on malbec1

This page was generated on 2017-04-15 16:10:21 -0400 (Sat, 15 Apr 2017).

Package 809/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSnbase 2.0.2
Laurent Gatto
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/MSnbase
Last Changed Rev: 125635 / Revision: 128728
Last Changed Date: 2017-01-04 08:17:27 -0500 (Wed, 04 Jan 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64 [ OK ] OK  ERROR 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MSnbase
Version: 2.0.2
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD INSTALL MSnbase
StartedAt: 2017-04-14 18:11:17 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 18:11:41 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 24.3 seconds
RetCode: 0
Status:  OK 

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD INSTALL MSnbase
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.4-bioc/R/library’
* installing *source* package ‘MSnbase’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c Spectrum1_class.c -o Spectrum1_class.o
Spectrum1_class.c:8:13: warning: ‘_new_Spectrum1’ defined but not used [-Wunused-function]
 static SEXP _new_Spectrum1(SEXP msLevel, SEXP peaksCount, SEXP rt,
             ^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c Spectrum2_class.c -o Spectrum2_class.o
Spectrum2_class.c:9:13: warning: ‘_new_Spectrum2’ defined but not used [-Wunused-function]
 static SEXP _new_Spectrum2(SEXP msLevel, SEXP peaksCount, SEXP rt,
             ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c utils.c -o utils.o
utils.c: In function ‘compar_double_dd_for_stable_asc_order’:
utils.c:92:15: warning: unused variable ‘ret’ [-Wunused-variable]
   int i1, i2, ret;
               ^
utils.c: In function ‘compar_double_dd_for_stable_desc_order’:
utils.c:107:15: warning: unused variable ‘ret’ [-Wunused-variable]
   int i1, i2, ret;
               ^
utils.c: In function ‘compar_double_asc_order’:
utils.c:123:18: warning: unused variable ‘ret’ [-Wunused-variable]
   double d1, d2, ret;
                  ^
utils.c: In function ‘compar_double_desc_order’:
utils.c:133:18: warning: unused variable ‘ret’ [-Wunused-variable]
   double d1, d2, ret;
                  ^
utils.c: At top level:
utils.c:121:12: warning: ‘compar_double_asc_order’ defined but not used [-Wunused-function]
 static int compar_double_asc_order(const void *p1, const void *p2)
            ^
utils.c:131:12: warning: ‘compar_double_desc_order’ defined but not used [-Wunused-function]
 static int compar_double_desc_order(const void *p1, const void *p2)
            ^
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o MSnbase.so RcppExports.o Spectrum1_class.o Spectrum2_class.o imp_neighbour_avg.o utils.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/R/library/MSnbase/libs
** R
** data
*** moving datasets to lazyload DB
Creating a new generic function for ‘smooth’ in package ‘MSnbase’
Creating a new generic function for ‘trimws’ in package ‘MSnbase’
in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra”
** inst
** preparing package for lazy loading
Creating a new generic function for ‘smooth’ in package ‘MSnbase’
Creating a new generic function for ‘trimws’ in package ‘MSnbase’
in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra”
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘benchmarking.Rmd’ 
   ‘MSnbase-demo.Rnw’ 
   ‘MSnbase-development.Rnw’ 
   ‘MSnbase-io.Rnw’ 
** testing if installed package can be loaded
* DONE (MSnbase)