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: 2017-10-18 05:21:56 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 05:33:32 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 696.1 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 3.4.2 (2017-09-28)
* 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    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      290.495 24.679 326.458
singlelinc-methods   77.294  6.705  86.743
clusterlinc-methods  18.937  0.386  19.861
linc-methods          6.177  0.348   6.691
plotlinc-methods      5.586  0.194   5.946
* 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	4.449	0.112	4.672
BRAIN_EXPR	0.178	0.020	0.200
LINCbio-class	0.002	0.000	0.002
LINCcluster-class	0.001	0.000	0.001
LINCfeature-class	0.001	0.000	0.000
LINCmatrix-class	0.001	0.000	0.001
LINCsingle-class	0.001	0.000	0.000
assignment-methods	0.189	0.026	0.217
changeOrgDb	0.179	0.017	0.200
clusterlinc-methods	18.937	0.386	19.861
correlation-methods	0.237	0.069	0.313
express-methods	0.305	0.156	0.471
feature	1.804	0.072	1.925
getbio-methods	290.495	24.679	326.458
getcoexpr	0.480	0.029	0.521
getlinc-methods	0.219	0.017	0.240
history-methods	0.175	0.016	0.195
justlinc-methods	0.002	0.001	0.002
linCenvir-methods	0.178	0.013	0.196
linc-methods	6.177	0.348	6.691
linctable-methods	0.000	0.000	0.001
plotlinc-methods	5.586	0.194	5.946
querycluster	0.491	0.017	0.522
results-methods	0.179	0.015	0.198
singlelinc-methods	77.294	6.705	86.743