Package: GeneGeneInteR

Version: 1.10.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GeneGeneInteR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GeneGeneInteR_1.10.0.tar.gz

StartedAt: 2019-10-16 01:50:44 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 01:56:38 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 353.7 seconds

RetCode: 0

Status:  OK

CheckDir: GeneGeneInteR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GeneGeneInteR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GeneGeneInteR_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/GeneGeneInteR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneGeneInteR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneGeneInteR’ version ‘1.10.0’
* 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 ‘GeneGeneInteR’ 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 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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... 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-3.9-bioc/meat/GeneGeneInteR.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL GeneGeneInteR
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘GeneGeneInteR’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c chclust.cpp -o chclust.o
chclust.cpp: In function ‘bool Conslink(long int, double**, double**)’:
chclust.cpp:82:29: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false [-Wstrict-overflow]
 #define dc(a,b)  (((a) > (b)) ? (DPtr[(a)-1][(b)-1]) : (DPtr[(b)-1][(a)-1]))
                             ^
chclust.cpp:306:18: note: in expansion of macro ‘dc’
       diag[i] =  dc(i,i+1);
                  ^~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o GeneGeneInteR.so chclust.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-GeneGeneInteR/00new/GeneGeneInteR/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (GeneGeneInteR)

name	user	system	elapsed
CCA.test	1.416	0.008	1.424
CLD.test	1.017	0.028	1.045
GBIGM.test	4.383	0.100	4.483
GGI	1.494	0.008	1.518
KCCA.test	0.002	0.000	0.001
PCA.test	0.05	0.00	0.05
PLSPM.test	2.502	0.008	2.509
gates.test	0.266	0.000	0.265
importFile	0.460	0.000	0.484
imputeSnpMatrix	0.757	0.008	0.769
minP.test	0.463	0.000	0.463
plot.GGInetwork	0.081	0.004	0.085
print.GGItest	0.018	0.000	0.018
selectSnps	0.006	0.000	0.006
snpMatrixScour	0.031	0.000	0.030
summary.GGInetwork	0.000	0.004	0.005
summary.GGItest	0.016	0.000	0.016
tProd.test	0.292	0.000	0.292
tTS.test	0.410	0.000	0.411