triplex 1.12.0
Jiri Hon
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/triplex | | Last Changed Rev: 117079 / Revision: 122332 | | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / 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 triplex_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/triplex.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘triplex/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘triplex’ version ‘1.12.0’
* 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 ‘triplex’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘rgl’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘S4Vectors’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘IRanges:::new_Views’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
TriplexViews: no visible global function definition for ‘DataFrame’
countBend: no visible global function definition for ‘optimize’
drawBase: no visible global function definition for ‘rgl.triangles’
join: no visible global function definition for ‘rgl.quads’
joinRect: no visible global function definition for ‘rgl.quads’
triplex.3D: no visible global function definition for
‘installed.packages’
triplex.3D: no visible global function definition for ‘nlm’
triplex.3D: no visible global function definition for ‘rgl.bg’
triplex.3D: no visible global function definition for ‘rgl.spheres’
Undefined global functions or variables:
DataFrame installed.packages nlm optimize rgl.bg rgl.quads
rgl.spheres rgl.triangles
Consider adding
importFrom("stats", "nlm", "optimize")
importFrom("utils", "installed.packages")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.3-bioc/meat/triplex.Rcheck/00check.log’
for details.
* installing *source* package ‘triplex’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -fPIC -Wall -mtune=core2 -g -O2 -c Biostrings_stubs.c -o Biostrings_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -fPIC -Wall -mtune=core2 -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -fPIC -Wall -mtune=core2 -g -O2 -c R_init_triplex.c -o R_init_triplex.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -fPIC -Wall -mtune=core2 -g -O2 -c XVector_stubs.c -o XVector_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -fPIC -Wall -mtune=core2 -g -O2 -c align.c -o align.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -fPIC -Wall -mtune=core2 -g -O2 -c align_interface.c -o align_interface.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -fPIC -Wall -mtune=core2 -g -O2 -c dl_list.c -o dl_list.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -fPIC -Wall -mtune=core2 -g -O2 -c interval.c -o interval.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -fPIC -Wall -mtune=core2 -g -O2 -c libtriplex.c -o libtriplex.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -fPIC -Wall -mtune=core2 -g -O2 -c progress.c -o progress.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -fPIC -Wall -mtune=core2 -g -O2 -c search.c -o search.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -fPIC -Wall -mtune=core2 -g -O2 -c search_interface.c -o search_interface.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 triplex.so Biostrings_stubs.o IRanges_stubs.o R_init_triplex.o XVector_stubs.o align.o align_interface.o dl_list.o interval.o libtriplex.o progress.o search.o search_interface.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.3-bioc/meat/triplex.Rcheck/triplex/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (triplex)