Package: CNORdt

Version: 1.24.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CNORdt.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CNORdt_1.24.1.tar.gz

StartedAt: 2019-04-15 23:05:49 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 23:07:53 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 124.5 seconds

RetCode: 0

Status:  OK

CheckDir: CNORdt.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CNORdt.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CNORdt_1.24.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/CNORdt.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNORdt/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNORdt’ version ‘1.24.1’
* 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 ‘CNORdt’ 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 ... NOTE
Package in Depends field not imported from: ‘abind’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
gaBinaryDT: no visible global function definition for ‘runif’
getFitDT: no visible global function definition for ‘splinefun’
getFitDT: no visible global function definition for ‘optim’
shift: no visible global function definition for ‘tail’
shift: no visible global function definition for ‘head’
Undefined global functions or variables:
  head optim runif splinefun tail
Consider adding
  importFrom("stats", "optim", "runif", "splinefun")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
cutAndPlotResultsDT 30.705  0.151  31.175
gaBinaryDT          29.722  0.081  30.100
* 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
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/CNORdt.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CNORdt
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘CNORdt’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c simulatorDT.c -o simulatorDT.o
simulatorDT.c:243:19: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
                        if((track_cond == nCond)) {
                            ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
simulatorDT.c:243:19: note: remove extraneous parentheses around the comparison to silence this warning
                        if((track_cond == nCond)) {
                           ˜           ^       ˜
simulatorDT.c:243:19: note: use '=' to turn this equality comparison into an assignment
                        if((track_cond == nCond)) {
                                       ^˜
                                       =
simulatorDT.c:55:6: warning: unused variable 'nTimes' [-Wunused-variable]
        int nTimes = INTEGER(nTimes_in)[0];
            ^
simulatorDT.c:53:6: warning: unused variable 'nSignals' [-Wunused-variable]
        int nSignals = INTEGER(nSignals_in)[0];
            ^
3 warnings generated.
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 CNORdt.so simulatorDT.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/CNORdt/libs
** R
** data
** 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
* DONE (CNORdt)

name	user	system	elapsed
computeScoreDT	0.151	0.021	0.175
convert2array	0.012	0.002	0.014
cutAndPlotResultsDT	30.705	0.151	31.175
gaBinaryDT	29.722	0.081	30.100
getFitDT	0.061	0.001	0.063
simulatorDT	0.012	0.001	0.014