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BioC 3.1: CHECK report for affyPLM on zin2

This page was generated on 2015-10-09 09:22:35 -0700 (Fri, 09 Oct 2015).

Package 25/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affyPLM 1.44.0
Ben Bolstad
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/affyPLM
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  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: affyPLM
Version: 1.44.0
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings affyPLM_1.44.0.tar.gz
StartedAt: 2015-10-08 22:22:22 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 22:26:07 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 224.5 seconds
RetCode: 0
Status:  OK 
CheckDir: affyPLM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings affyPLM_1.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/affyPLM.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affyPLM/DESCRIPTION’ ... OK
* this is package ‘affyPLM’ version ‘1.44.0’
* 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 ‘affyPLM’ can be installed ... [13s/13s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘BiocGenerics’
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 dependencies in R code ... NOTE
'library' or 'require' call to ‘stats’ which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
image,PLMset : .local: warning in layout(matrix(c(1, 2), 1, 2), width =
  c(9, 1)): partial argument match of 'width' to 'widths'
show,PLMset: warning in ls(env = cdf.env): partial argument match of
  'env' to 'envir'
* checking Rd files ... NOTE
prepare_Rd: MAplot.Rd:11-13: Dropping empty section \usage
* 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 ... [52s/52s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
threestep      21.903  0.220  22.240
fitPLM         12.095  0.140  12.269
PLMset2exprSet  6.939  0.084   7.018
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘C_code_tests.R’ [3s/3s]
  Running ‘PLM_tests.R’ [0s/0s]
  Running ‘preprocess_tests.R’ [23s/23s]
  Running ‘threestepPLM_tests.R’ [66s/67s]
 [94s/94s] 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.1-bioc/meat/affyPLM.Rcheck/00check.log’
for details.


affyPLM.Rcheck/00install.out:

* installing *source* package ‘affyPLM’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c LESN.c -o LESN.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c PLM_avg_log.c -o PLM_avg_log.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c PLM_biweight.c -o PLM_biweight.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c PLM_log_avg.c -o PLM_log_avg.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c PLM_medianPM.c -o PLM_medianPM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c SCAB.c -o SCAB.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c common_types.c -o common_types.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c do_PLMrlm.c -o do_PLMrlm.o
do_PLMrlm.c: In function ‘do_PLM_rlm’:
do_PLMrlm.c:620:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable]
   int first_ind;
       ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c do_PLMrma.c -o do_PLMrma.o
do_PLMrma.c: In function ‘do_PLMrma’:
do_PLMrma.c:209:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable]
   int first_ind;
       ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c do_PLMthreestep.c -o do_PLMthreestep.o
do_PLMthreestep.c: In function ‘do_PLMthreestep’:
do_PLMthreestep.c:118:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable]
   int first_ind;
       ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c idealmismatch.c -o idealmismatch.o
idealmismatch.c: In function ‘IdealMM_correct_single’:
idealmismatch.c:71:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable]
   int first_ind;
       ^
idealmismatch.c: In function ‘SpecificBiweightCorrect_single’:
idealmismatch.c:183:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable]
   int first_ind;
       ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c lm_threestep.c -o lm_threestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c matrix_functions.c -o matrix_functions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c nthLargestPM.c -o nthLargestPM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c preprocess.c -o preprocess.o
preprocess.c: In function ‘pp_background’:
preprocess.c:158:7: warning: variable ‘which_lesn’ set but not used [-Wunused-but-set-variable]
   int which_lesn;
       ^
preprocess.c: In function ‘pp_bothstages’:
preprocess.c:677:12: warning: variable ‘cols’ set but not used [-Wunused-but-set-variable]
   int rows,cols;
            ^
preprocess.c:677:7: warning: variable ‘rows’ set but not used [-Wunused-but-set-variable]
   int rows,cols;
       ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c psi_fns.c -o psi_fns.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c qnorm_probeset.c -o qnorm_probeset.o
qnorm_probeset.c: In function ‘qnorm_probeset_c’:
qnorm_probeset.c:110:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable]
   int first_ind;
       ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c read_rmaexpress.c -o read_rmaexpress.o
read_rmaexpress.c: In function ‘gzfread_int32’:
read_rmaexpress.c:375:3: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
   result = gzread(instream,destination,sizeof(int)*n);
   ^
In file included from read_rmaexpress.c:31:0:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
                     ^
read_rmaexpress.c: In function ‘gzfread_float64’:
read_rmaexpress.c:395:3: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
   result = gzread(instream,destination,sizeof(double)*n);
   ^
In file included from read_rmaexpress.c:31:0:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
                     ^
read_rmaexpress.c: In function ‘gzfread_char’:
read_rmaexpress.c:412:3: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
   result =  gzread(instream,destination,sizeof(char)*n);
   ^
In file included from read_rmaexpress.c:31:0:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
                     ^
read_rmaexpress.c: In function ‘gz_read_rmaexpress_header’:
read_rmaexpress.c:456:15: warning: assignment from incompatible pointer type [enabled by default]
   currentFile = gzopen(filename,mode);
               ^
read_rmaexpress.c: In function ‘gz_read_rmaexpress’:
read_rmaexpress.c:575:15: warning: assignment from incompatible pointer type [enabled by default]
   currentFile = gzopen(filename,mode);
               ^
read_rmaexpress.c: In function ‘isCompressedRMAExpress’:
read_rmaexpress.c:719:15: warning: assignment from incompatible pointer type [enabled by default]
   currentFile = gzopen(filename,mode);
               ^
read_rmaexpress.c:731:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
   gzclose(currentFile);
   ^
In file included from read_rmaexpress.c:31:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
                        ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c rlm_PLM.c -o rlm_PLM.o
rlm_PLM.c: In function ‘R_rlm_PLMset_c’:
rlm_PLM.c:1481:12: warning: variable ‘cols’ set but not used [-Wunused-but-set-variable]
   int rows,cols;
            ^
rlm_PLM.c:1481:7: warning: variable ‘rows’ set but not used [-Wunused-but-set-variable]
   int rows,cols;
       ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c rlm_threestep.c -o rlm_threestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c rma_PLM.c -o rma_PLM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c rma_common.c -o rma_common.o
rma_common.c: In function ‘median’:
rma_common.c:60:7: warning: unused variable ‘i’ [-Wunused-variable]
   int i;
       ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c scaling.c -o scaling.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c threestep.c -o threestep.o
threestep.c: In function ‘threestep_summary’:
threestep.c:82:15: warning: variable ‘MM’ set but not used [-Wunused-but-set-variable]
   double *PM,*MM;
               ^
threestep.c: In function ‘R_threestep_c’:
threestep.c:193:12: warning: variable ‘cols’ set but not used [-Wunused-but-set-variable]
   int rows,cols;
            ^
threestep.c:193:7: warning: variable ‘rows’ set but not used [-Wunused-but-set-variable]
   int rows,cols;
       ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c threestep_PLM.c -o threestep_PLM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c threestep_common.c -o threestep_common.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c threestep_summary.c -o threestep_summary.o
threestep_summary.c: In function ‘do_3summary’:
threestep_summary.c:73:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable]
   int first_ind;
       ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c transfns.c -o transfns.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o affyPLM.so LESN.o PLM_avg_log.o PLM_biweight.o PLM_log_avg.o PLM_medianPM.o PLM_median_logPM.o PLM_medianpolish.o PLM_modelmatrix.o SCAB.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o lm_threestep.o matrix_functions.o nthLargestPM.o preprocess.o psi_fns.o qnorm_probeset.o read_rmaexpress.o rlm_PLM.o rlm_threestep.o rmaPLM_pseudo.o rma_PLM.o rma_common.o scaling.o threestep.o threestep_PLM.o threestep_common.o threestep_summary.o threestep_summary_methods.o transfns.o -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.1-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.1-bioc/R/lib -lRblas -lz -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-bioc/meat/affyPLM.Rcheck/affyPLM/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘summary’ from package ‘base’ in package ‘affyPLM’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (affyPLM)

affyPLM.Rcheck/affyPLM-Ex.timings:

nameusersystemelapsed
PLMset2exprSet6.9390.0847.018
bg.correct.LESN1.3060.0121.318
fitPLM12.095 0.14012.269
normalize.exprSet1.4710.0041.483
normalize.scaling1.3230.0081.332
preprocess2.5310.0402.582
rmaPLM0.2600.0080.267
threestep21.903 0.22022.240
threestepPLM0.2780.0040.281