Package: Vega

Version: 1.34.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Vega.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Vega_1.34.0.tar.gz

StartedAt: 2020-04-15 06:23:48 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:24:11 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 22.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Vega.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Vega.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Vega_1.34.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/Vega.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Vega/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Vega’ version ‘1.34.0’
* 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 ‘Vega’ can be installed ... WARNING
Found the following significant warnings:
  vega.c:369:20: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Users/biocbuild/bbs-3.10-bioc/meat/Vega.Rcheck/00install.out’ for details.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotSegmentation: no visible global function definition for ‘par’
plotSegmentation: no visible global function definition for ‘plot’
plotSegmentation: no visible global function definition for ‘lines’
vega: no visible global function definition for ‘sd’
vega: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  lines par plot sd write.table
Consider adding
  importFrom("graphics", "lines", "par", "plot")
  importFrom("stats", "sd")
  importFrom("utils", "write.table")
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
* 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/Vega.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 Vega
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘Vega’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c vega.c -o vega.o
vega.c:369:20: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
        lambda_gradient = abs(lambda);
                          ^
vega.c:369:20: note: use function 'fabs' instead
        lambda_gradient = abs(lambda);
                          ^~~
                          fabs
vega.c:355:13: warning: unused variable 'maxptr' [-Wunused-variable]
        node max, *maxptr, tmp_node;
                   ^
vega.c:348:68: warning: unused variable 'tmp_lambda2' [-Wunused-variable]
        double lambda, lambda_gradient, stop_lambda_gradient, tmp_lambda, tmp_lambda2;
                                                                          ^
vega.c:347:6: warning: unused variable 'index' [-Wunused-variable]
        int index;
            ^
vega.c:560:64: warning: unused variable 'next_mean' [-Wunused-variable]
        double lambda, first_term, second_term, prev_mean, curr_mean, next_mean;
                                                                      ^
5 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 Vega.so vega.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-Vega/00new/Vega/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Vega)

name	user	system	elapsed
Vega-package	0.312	0.025	0.342
plotSegmentation	0.618	0.076	0.773
vega	0.205	0.011	0.221