XVector 0.4.0
H. Pages
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/XVector | | Last Changed Rev: 88838 / Revision: 95116 | | Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | WARNINGS | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK |
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### Running command:
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### /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings XVector_0.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/XVector.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘XVector/DESCRIPTION’ ... OK
* this is package ‘XVector’ version ‘0.4.0’
* 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 ‘XVector’ can be installed ... [7s/8s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘methods’ ‘BiocGenerics’ ‘IRanges’
A package should be listed in only one of these fields.
* 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
Unexported objects imported by ':::' calls:
‘BiocGenerics:::testPackage’ ‘IRanges:::disableValidity’
‘IRanges:::extractROWS’ ‘IRanges:::normalizeDoubleBracketSubscript’
‘IRanges:::rbind.mcols’ ‘IRanges:::setDefaultSlotValue’
‘IRanges:::solveUserSEWForSingleSeq’ ‘IRanges:::toNumSnippet’
See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 ... WARNING
Undocumented code objects:
‘RdaCollection’ ‘rdaPath’
Undocumented S4 classes:
‘RdaCollection’
Undocumented S4 methods:
generic '[[' and siglist 'RdaCollection'
generic 'extractList' and siglist 'XVector,Ranges'
generic 'length' and siglist 'RdaCollection'
generic 'names' and siglist 'RdaCollection'
generic 'rdaPath' and siglist 'RdaCollection'
generic 'relist' and siglist 'XVector,PartitioningByEnd'
generic 'relistToClass' and siglist 'XVector'
generic 'splitAsListReturnedClass' and siglist 'XVector'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking examples ... [9s/9s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
reverse-methods 5.04 0.068 5.127
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘run_unitTests.R’ [3s/3s]
[3s/3s] OK
* checking PDF version of manual ... OK
WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
‘/home/biocbuild/bbs-2.14-bioc/meat/XVector.Rcheck/00check.log’
for details.
* installing *source* package ‘XVector’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c R_init_XVector.c -o R_init_XVector.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c SharedDouble_class.c -o SharedDouble_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c SharedInteger_class.c -o SharedInteger_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c SharedRaw_class.c -o SharedRaw_class.o
SharedRaw_class.c: In function ‘SharedRaw_read_complexes_from_subscript’:
SharedRaw_class.c:364:13: warning: variable ‘src_tag’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c SharedVector_class.c -o SharedVector_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c XRawList_comparison.c -o XRawList_comparison.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c XVectorList_class.c -o XVectorList_class.o
XVectorList_class.c: In function ‘_new_XRawList_from_CharAEAE’:
XVectorList_class.c:465:33: warning: ‘lkup_length’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c XVector_class.c -o XVector_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c slice_methods.c -o slice_methods.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c vector_copy.c -o vector_copy.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c view_summarization_methods.c -o view_summarization_methods.o
view_summarization_methods.c: In function ‘get_which_min_from_Ints_holder’:
view_summarization_methods.c:219:36: warning: ‘cur_min’ may be used uninitialized in this function [-Wuninitialized]
view_summarization_methods.c: In function ‘get_which_max_from_Ints_holder’:
view_summarization_methods.c:269:36: warning: ‘cur_max’ may be used uninitialized in this function [-Wuninitialized]
view_summarization_methods.c: In function ‘get_which_max_from_Doubles_holder’:
view_summarization_methods.c:296:36: warning: ‘cur_max’ may be used uninitialized in this function [-Wuninitialized]
view_summarization_methods.c: In function ‘get_which_min_from_Doubles_holder’:
view_summarization_methods.c:246:36: warning: ‘cur_min’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -shared -L/usr/local/lib -o XVector.so IRanges_stubs.o Ocopy_byteblocks.o R_init_XVector.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o XRawList_comparison.o XVectorList_class.o XVector_class.o slice_methods.o vector_copy.o view_summarization_methods.o -L/home/biocbuild/bbs-2.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.14-bioc/meat/XVector.Rcheck/XVector/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘toString’ from package ‘base’ in package ‘XVector’
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (XVector)