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BioC 3.1: CHECK report for VegaMC on morelia

This page was generated on 2015-10-09 09:40:16 -0700 (Fri, 09 Oct 2015).

Package 1008/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VegaMC 3.6.0
Sandro Morganella
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/VegaMC
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: VegaMC
Version: 3.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings VegaMC_3.6.0.tar.gz
StartedAt: 2015-10-09 07:09:01 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 07:10:48 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 106.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: VegaMC.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings VegaMC_3.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/VegaMC.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘VegaMC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘VegaMC’ version ‘3.6.0’
* 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 ‘VegaMC’ can be installed ... [11s/12s] OK
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    example   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 ... NOTE
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
File ‘VegaMC/libs/VegaMC.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘run_vegaMC.o’

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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [4s/5s] WARNING
Found the following significant warnings:

  Warning: 'sampleNames' is deprecated.
  Warning: 'sampleNames' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/VegaMC.Rcheck/00check.log’
for details.


VegaMC.Rcheck/00install.out:

* installing *source* package ‘VegaMC’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c run_vegaMC.c -o run_vegaMC.o
run_vegaMC.c:491:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion]
            elem = strtok('\0', sep);
                          ^˜˜˜
run_vegaMC.c:526:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion]
            elem = strtok('\0', sep);
                          ^˜˜˜
run_vegaMC.c:618:18: warning: unused variable 'brkt' [-Wunused-variable]
    char *elem, *brkt;
                 ^
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c sort_data.c -o sort_data.o
sort_data.c:131:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion]
            elem = strtok('\0', sep);
                          ^˜˜˜
sort_data.c:180:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion]
            elem = strtok('\0', sep);
                          ^˜˜˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c vegaMC.c -o vegaMC.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 VegaMC.so run_vegaMC.o sort_data.o vegaMC.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-bioc/meat/VegaMC.Rcheck/VegaMC/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (VegaMC)

VegaMC.Rcheck/VegaMC-Ex.timings:

nameusersystemelapsed
VegaMC-package0.1140.0150.145
sortData0.1890.0120.200
vegaMC-methods0.2720.0370.543