BioC 3.5: CHECK report for LINC on malbec2

Package: LINC

Version: 1.4.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings LINC_1.4.0.tar.gz

StartedAt: 2017-10-18 00:22:09 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:31:37 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 568.6 seconds

RetCode: 0

Status:  OK

CheckDir: LINC.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings LINC_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/LINC.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 ‘LINC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘LINC’ version ‘1.4.0’
* 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 ‘LINC’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   1.4Mb
* 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 ... 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 R/sysdata.rda ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
              old_size new_size compress
  sysdata.rda    449Kb    313Kb       xz
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
getbio-methods      252.660  7.804 260.823
singlelinc-methods   70.788  1.508  72.347
clusterlinc-methods  14.424  0.076  14.503
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/LINC.Rcheck/00check.log’
for details.

* installing *source* package ‘LINC’ ...
** libs
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c Cppspear.cpp -o Cppspear.o
Cppspear.cpp: In function ‘Rcpp::NumericMatrix Cppspear(Rcpp::NumericMatrix, Rcpp::NumericMatrix)’:
Cppspear.cpp:78:14: warning: unused variable ‘qspear’ [-Wunused-variable]
       double qspear;double nfraction;
              ^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c LINC_init.c -o LINC_init.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c docdd.cpp -o docdd.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c doesd.cpp -o doesd.o
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o LINC.so Cppspear.o LINC_init.o RcppExports.o docdd.o doesd.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/LINC.Rcheck/LINC/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘history’ in package ‘LINC’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (LINC)

name	user	system	elapsed
Arith-methods	3.944	0.036	3.982
BRAIN_EXPR	0.168	0.016	0.184
LINCbio-class	0.000	0.000	0.001
LINCcluster-class	0.000	0.000	0.001
LINCfeature-class	0.000	0.000	0.001
LINCmatrix-class	0.004	0.000	0.000
LINCsingle-class	0.000	0.000	0.001
assignment-methods	0.176	0.000	0.175
changeOrgDb	0.172	0.000	0.173
clusterlinc-methods	14.424	0.076	14.503
correlation-methods	0.196	0.028	0.227
express-methods	0.256	0.068	0.326
feature	1.464	0.020	1.482
getbio-methods	252.660	7.804	260.823
getcoexpr	0.412	0.008	0.423
getlinc-methods	0.2	0.0	0.2
history-methods	0.200	0.000	0.203
justlinc-methods	0.004	0.000	0.001
linCenvir-methods	0.160	0.000	0.161
linc-methods	4.748	0.004	4.753
linctable-methods	0	0	0
plotlinc-methods	3.740	0.000	3.741
querycluster	0.428	0.004	0.433
results-methods	0.160	0.000	0.161
singlelinc-methods	70.788	1.508	72.347