BioC 3.4: CHECK report for LINC on tokay1

Package: LINC

Version: 1.2.0

Command: rm -rf LINC.buildbin-libdir LINC.Rcheck && mkdir LINC.buildbin-libdir LINC.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=LINC.buildbin-libdir LINC_1.2.0.tar.gz >LINC.Rcheck\00install.out 2>&1 && cp LINC.Rcheck\00install.out LINC-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=LINC.buildbin-libdir --install="check:LINC-install.out" --force-multiarch --no-vignettes --timings LINC_1.2.0.tar.gz

StartedAt: 2017-04-14 23:13:43 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:34:45 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 1261.9 seconds

RetCode: 0

Status:  OK

CheckDir: LINC.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf LINC.buildbin-libdir LINC.Rcheck && mkdir LINC.buildbin-libdir LINC.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=LINC.buildbin-libdir LINC_1.2.0.tar.gz >LINC.Rcheck\00install.out 2>&1 && cp LINC.Rcheck\00install.out LINC-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=LINC.buildbin-libdir --install="check:LINC-install.out" --force-multiarch --no-vignettes --timings LINC_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/LINC.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'LINC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'LINC' version '1.2.0'
* 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 whether package 'LINC' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.4-bioc/meat/LINC.buildbin-libdir/LINC/libs/i386/LINC.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
getbio-methods      312.92  26.90  340.46
singlelinc-methods   85.09   5.47   90.61
clusterlinc-methods  14.42   0.10   14.51
linc-methods          5.28   0.13    5.41
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
getbio-methods      299.78  22.01  321.97
singlelinc-methods   76.84   4.64   81.50
clusterlinc-methods  16.50   0.09   16.59
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/LINC.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'LINC' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -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;
              ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c LINC_init.c -o LINC_init.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c docdd.cpp -o docdd.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c doesd.cpp -o doesd.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o LINC.dll tmp.def Cppspear.o LINC_init.o RcppExports.o docdd.o doesd.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/LINC.buildbin-libdir/LINC/libs/i386
** 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

install for x64

* installing *source* package 'LINC' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -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;
              ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c LINC_init.c -o LINC_init.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c docdd.cpp -o docdd.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c doesd.cpp -o doesd.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o LINC.dll tmp.def Cppspear.o LINC_init.o RcppExports.o docdd.o doesd.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/LINC.buildbin-libdir/LINC/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'LINC' as LINC_1.2.0.zip
* DONE (LINC)

name	user	system	elapsed
Arith-methods	3.11	0.11	3.22
BRAIN_EXPR	0.22	0.00	0.21
LINCbio-class	0	0	0
LINCcluster-class	0	0	0
LINCfeature-class	0	0	0
LINCmatrix-class	0	0	0
LINCsingle-class	0	0	0
assignment-methods	0.22	0.03	0.25
changeOrgDb	0.27	0.01	0.29
clusterlinc-methods	14.42	0.10	14.51
correlation-methods	0.25	0.06	0.31
express-methods	0.36	0.08	0.44
feature	1.55	0.08	1.63
getbio-methods	312.92	26.90	340.46
getcoexpr	0.45	0.00	0.46
getlinc-methods	0.20	0.02	0.22
history-methods	0.22	0.01	0.23
justlinc-methods	0	0	0
linCenvir-methods	0.22	0.00	0.22
linc-methods	5.28	0.13	5.41
linctable-methods	0	0	0
plotlinc-methods	4.54	0.06	4.61
querycluster	0.35	0.03	0.38
results-methods	0.19	0.01	0.20
singlelinc-methods	85.09	5.47	90.61

name	user	system	elapsed
Arith-methods	3.08	0.10	3.17
BRAIN_EXPR	0.20	0.00	0.21
LINCbio-class	0	0	0
LINCcluster-class	0	0	0
LINCfeature-class	0	0	0
LINCmatrix-class	0	0	0
LINCsingle-class	0	0	0
assignment-methods	0.19	0.01	0.20
changeOrgDb	0.17	0.02	0.19
clusterlinc-methods	16.50	0.09	16.59
correlation-methods	0.24	0.02	0.25
express-methods	0.33	0.06	0.39
feature	1.71	0.06	1.76
getbio-methods	299.78	22.01	321.97
getcoexpr	0.31	0.02	0.32
getlinc-methods	0.17	0.02	0.19
history-methods	0.17	0.00	0.17
justlinc-methods	0	0	0
linCenvir-methods	0.16	0.03	0.19
linc-methods	4.76	0.03	4.80
linctable-methods	0	0	0
plotlinc-methods	4.86	0.01	4.88
querycluster	0.34	0.02	0.36
results-methods	0.18	0.00	0.17
singlelinc-methods	76.84	4.64	81.50