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BioC 3.5: CHECK report for rqubic on malbec2

This page was generated on 2017-10-18 14:14:14 -0400 (Wed, 18 Oct 2017).

Package 1148/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rqubic 1.22.0
Jitao David Zhang
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/rqubic
Branch: RELEASE_3_5
Last Commit: c12d027
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: rqubic
Version: 1.22.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings rqubic_1.22.0.tar.gz
StartedAt: 2017-10-18 02:13:57 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 02:14:37 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 40.5 seconds
RetCode: 0
Status:  OK 
CheckDir: rqubic.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings rqubic_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/rqubic.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rqubic/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rqubic’ version ‘1.22.0’
* 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 ‘rqubic’ can be installed ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
writeQubicInputFile: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  write.table
Consider adding
  importFrom("utils", "write.table")
to your NAMESPACE file.
* 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 for GNU extensions in Makefiles ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘c_output_parser_tests.R’
  Running ‘rqubic_implementations.R’
  Running ‘test_read.R’
  Running ‘test_utilities.R’
 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/rqubic.Rcheck/00check.log’
for details.


rqubic.Rcheck/00install.out:

* installing *source* package ‘rqubic’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c bicluster.c -o bicluster.o
bicluster.c: In function ‘seed_intersect_r’:
bicluster.c:354:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
       if (flag=ss) (*m_cnt)++;
       ^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c discretize.c -o discretize.o
In file included from discretize.c:9:0:
rqubic.h:60:20: warning: ‘EDGELIST_ATT_NAME’ defined but not used [-Wunused-variable]
 static const char *EDGELIST_ATT_NAME="edgelist";
                    ^
rqubic.h:61:20: warning: ‘MINCOL_ATT_NAME’ defined but not used [-Wunused-variable]
 static const char *MINCOL_ATT_NAME="minimumCol";
                    ^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c fib.c -o fib.o
In file included from fib.c:35:0:
rqubic.h:60:20: warning: ‘EDGELIST_ATT_NAME’ defined but not used [-Wunused-variable]
 static const char *EDGELIST_ATT_NAME="edgelist";
                    ^
rqubic.h:61:20: warning: ‘MINCOL_ATT_NAME’ defined but not used [-Wunused-variable]
 static const char *MINCOL_ATT_NAME="minimumCol";
                    ^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c graph.c -o graph.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c rqubic.c -o rqubic.o
In file included from rqubic.c:5:0:
rqubic.h:60:20: warning: ‘EDGELIST_ATT_NAME’ defined but not used [-Wunused-variable]
 static const char *EDGELIST_ATT_NAME="edgelist";
                    ^
rqubic.h:61:20: warning: ‘MINCOL_ATT_NAME’ defined but not used [-Wunused-variable]
 static const char *MINCOL_ATT_NAME="minimumCol";
                    ^
gcc -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o rqubic.so bicluster.o discretize.o fib.o graph.o rqubic.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/rqubic.Rcheck/rqubic/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rqubic)

rqubic.Rcheck/rqubic-Ex.timings:

nameusersystemelapsed
QUBICBiclusterSet-class0.0040.0000.001
combineBiclusts-methods1.7680.0161.785
discretize0.0520.0000.050
eSetDimName0.0640.0000.063
fcFilter0.5320.0000.529
features-methods0.120.000.12
generateSeeds-methods0.0720.0000.070
parseQubicBlocks0.0960.0000.098
quBicluster0.5080.0000.510
readBiclusterResults0.0720.0000.069
writeQubicInputFile0.0600.0040.066