BioC 3.5: CHECK report for LINC on veracruz2

Package: LINC

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LINC_1.4.0.tar.gz

StartedAt: 2017-08-16 04:36:49 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 04:49:01 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 731.7 seconds

RetCode: 0

Status:  OK

CheckDir: LINC.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LINC_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/LINC.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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   4.9Mb
* 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    311Kb       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      312.606 24.368 348.422
singlelinc-methods   85.201  6.299  94.539
clusterlinc-methods  19.594  0.325  20.466
linc-methods          6.900  0.553   7.693
plotlinc-methods      4.964  0.193   5.310
Arith-methods         4.942  0.105   5.159
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/LINC.Rcheck/00check.log’
for details.

* installing *source* package ‘LINC’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c Cppspear.cpp -o Cppspear.o
Cppspear.cpp:78:14: warning: unused variable 'qspear' [-Wunused-variable]
      double qspear;double nfraction;
             ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c LINC_init.c -o LINC_init.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c docdd.cpp -o docdd.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c doesd.cpp -o doesd.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o LINC.so Cppspear.o LINC_init.o RcppExports.o docdd.o doesd.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/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	4.942	0.105	5.159
BRAIN_EXPR	0.171	0.016	0.197
LINCbio-class	0.001	0.000	0.001
LINCcluster-class	0.001	0.000	0.001
LINCfeature-class	0.001	0.000	0.001
LINCmatrix-class	0.001	0.000	0.001
LINCsingle-class	0.001	0.000	0.001
assignment-methods	0.167	0.017	0.184
changeOrgDb	0.182	0.012	0.198
clusterlinc-methods	19.594	0.325	20.466
correlation-methods	0.219	0.056	0.284
express-methods	0.289	0.138	0.436
feature	1.637	0.051	1.736
getbio-methods	312.606	24.368	348.422
getcoexpr	0.484	0.026	0.535
getlinc-methods	0.221	0.015	0.246
history-methods	0.197	0.014	0.216
justlinc-methods	0.002	0.000	0.002
linCenvir-methods	0.182	0.015	0.199
linc-methods	6.900	0.553	7.693
linctable-methods	0.000	0.000	0.001
plotlinc-methods	4.964	0.193	5.310
querycluster	0.512	0.018	0.552
results-methods	0.169	0.013	0.188
singlelinc-methods	85.201	6.299	94.539