MANOR 1.36.0
Pierre Neuvial
| 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/MANOR | | 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 | NotNeeded | OK | [ WARNINGS ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | 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 MANOR_1.36.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/MANOR.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 ‘MANOR/DESCRIPTION’ ... OK
* this is package ‘MANOR’ version ‘1.36.0’
* 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 ‘MANOR’ can be installed ... [3s/3s] WARNING
Found the following significant warnings:
Rnem_exe.c:216:20: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See ‘/home/biocbuild/bbs-2.14-bioc/meat/MANOR.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘GLAD’
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 loading without being on the library search path ... 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 ... 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 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 line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [9s/9s] 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
WARNING: There was 1 warning.
NOTE: There was 1 note.
See
‘/home/biocbuild/bbs-2.14-bioc/meat/MANOR.Rcheck/00check.log’
for details.
* installing *source* package ‘MANOR’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c Rnem_arg.c -o Rnem_arg.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c Rnem_exe.c -o Rnem_exe.o
Rnem_exe.c: In function ‘MakeErrinfo’:
Rnem_exe.c:216:20: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c exememo.c -o exememo.o
exememo.c: In function ‘GenAlloc’:
exememo.c:42:7: warning: passing argument 1 of ‘Rf_error’ makes pointer from integer without a cast [enabled by default]
/home/biocbuild/bbs-2.14-bioc/R/include/R_ext/Error.h:33:6: note: expected ‘const char *’ but argument is of type ‘int’
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c lib_io.c -o lib_io.o
lib_io.c: In function ‘AskFloat’:
lib_io.c:284:13: warning: ignoring return value of ‘gets’, declared with attribute warn_unused_result [-Wunused-result]
lib_io.c: In function ‘AskInteger’:
lib_io.c:236:13: warning: ignoring return value of ‘gets’, declared with attribute warn_unused_result [-Wunused-result]
lib_io.c: In function ‘AskFileToWrite’:
lib_io.c:159:13: warning: ignoring return value of ‘gets’, declared with attribute warn_unused_result [-Wunused-result]
lib_io.c: In function ‘AskFileToRead’:
lib_io.c:108:13: warning: ignoring return value of ‘gets’, declared with attribute warn_unused_result [-Wunused-result]
lib_io.c: In function ‘ReadOpeningComments’:
lib_io.c:83:14: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
In file included from /usr/include/stdio.h:934:0,
from lib_io.c:17:
In function ‘gets’,
inlined from ‘AskFileToRead’ at lib_io.c:108:13:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:230:3: warning: call to ‘__gets_warn’ declared with attribute warning: please use fgets or getline instead, gets can't specify buffer size [enabled by default]
In function ‘gets’,
inlined from ‘AskFileToWrite’ at lib_io.c:159:13:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:230:3: warning: call to ‘__gets_warn’ declared with attribute warning: please use fgets or getline instead, gets can't specify buffer size [enabled by default]
lib_io.c: In function ‘CountLinesColumns’:
lib_io.c:400:16: warning: ‘mincols’ 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 -fpic -g -O2 -Wall -c nem_alg.c -o nem_alg.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c nem_hlp.c -o nem_hlp.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c nem_mod.c -o nem_mod.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c nem_nei.c -o nem_nei.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c nem_rnd.c -o nem_rnd.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c nem_ver.c -o nem_ver.o
gcc -std=gnu99 -shared -L/usr/local/lib -o MANOR.so Rnem_arg.o Rnem_exe.o exememo.o lib_io.o nem_alg.o nem_hlp.o nem_mod.o nem_nei.o nem_rnd.o nem_ver.o -L/home/biocbuild/bbs-2.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.14-bioc/meat/MANOR.Rcheck/MANOR/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MANOR)