iBBiG 1.19.0
Aedin Culhane
| Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/iBBiG | | Last Changed Rev: 122712 / Revision: 129046 | | Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings iBBiG_1.19.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/iBBiG.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iBBiG/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iBBiG’ version ‘1.19.0’
* 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 ‘iBBiG’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
'library' or 'require' call to ‘biclust’ which was already attached by Depends.
Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addSignal: no visible global function definition for ‘runif’
iBBiG: no visible global function definition for ‘new’
makeArtificial: no visible global function definition for ‘runif’
makeArtificial: no visible global function definition for ‘new’
Clusterscores,iBBiG: no visible global function definition for ‘slot’
Clusterscores<-,iBBiG: no visible global function definition for
‘slot<-’
Clusterscores<-,iBBiG: no visible global function definition for
‘validObject’
Number,iBBiG: no visible global function definition for ‘slot’
Number<-,iBBiG: no visible global function definition for ‘slot<-’
Number<-,iBBiG: no visible global function definition for ‘validObject’
NumberxCol,iBBiG: no visible global function definition for ‘slot’
NumberxCol<-,iBBiG: no visible global function definition for ‘slot<-’
NumberxCol<-,iBBiG: no visible global function definition for
‘validObject’
Parameters,iBBiG: no visible global function definition for ‘slot’
Parameters<-,iBBiG: no visible global function definition for ‘slot<-’
Parameters<-,iBBiG: no visible global function definition for
‘validObject’
RowScorexNumber,iBBiG: no visible global function definition for ‘slot’
RowScorexNumber<-,iBBiG: no visible global function definition for
‘slot<-’
RowScorexNumber<-,iBBiG: no visible global function definition for
‘validObject’
RowxNumber,iBBiG: no visible global function definition for ‘slot’
RowxNumber<-,iBBiG: no visible global function definition for ‘slot<-’
RowxNumber<-,iBBiG: no visible global function definition for
‘validObject’
Seeddata,iBBiG: no visible global function definition for ‘slot’
Seeddata<-,iBBiG: no visible global function definition for ‘slot<-’
Seeddata<-,iBBiG: no visible global function definition for
‘validObject’
analyzeClust,Biclust-iBBiG: no visible global function definition for
‘as’
analyzeClust,list-iBBiG: no visible global function definition for
‘new’
coerce,Biclust-iBBiG: no visible global function definition for ‘new’
info,iBBiG: no visible global function definition for ‘slot’
info<-,iBBiG: no visible global function definition for ‘slot<-’
info<-,iBBiG: no visible global function definition for ‘validObject’
plot,iBBiG-ANY: no visible global function definition for ‘layout’
plot,iBBiG-ANY: no visible global function definition for ‘colors’
plot,iBBiG-ANY: no visible global function definition for ‘image’
plot,iBBiG-ANY: no visible global function definition for ‘legend’
plot,iBBiG-ANY: no visible binding for global variable ‘title’
plot,iBBiG-ANY: no visible global function definition for ‘title’
plot,iBBiG-ANY: no visible global function definition for ‘barplot’
Undefined global functions or variables:
as barplot colors image layout legend new runif slot slot<- title
validObject
Consider adding
importFrom("grDevices", "colors")
importFrom("graphics", "barplot", "image", "layout", "legend", "title")
importFrom("methods", "as", "new", "slot", "slot<-", "validObject")
importFrom("stats", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ‘iBBiG/libs/iBBiG.so’:
Found ‘_rand’, possibly from ‘rand’ (C)
Object: ‘iBBiG.o’
Found ‘_srand’, possibly from ‘srand’ (C)
Object: ‘iBBiG.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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
iBBiG-package 27.152 0.119 27.648
iBBiG 25.736 0.093 26.135
iBBiG-class 25.170 0.124 25.683
* 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: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/iBBiG.Rcheck/00check.log’
for details.
* installing *source* package ‘iBBiG’ ...
** 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 R_init_iBBiG.c -o R_init_iBBiG.o
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 iBBiG.c -o iBBiG.o
iBBiG.c:300:22: warning: implicit declaration of function 'time' is invalid in C99 [-Wimplicit-function-declaration]
srand((unsigned)time(NULL));
^
1 warning 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 iBBiG.so R_init_iBBiG.o iBBiG.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/iBBiG.Rcheck/iBBiG/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (iBBiG)