MANOR 1.48.0
Pierre Neuvial
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/MANOR | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | 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 MANOR_1.48.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/MANOR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MANOR/DESCRIPTION’ ... OK
* this is package ‘MANOR’ version ‘1.48.0’
* 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 ... OK
* 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 compiled code ... NOTE
File ‘MANOR/libs/MANOR.so’:
Found ‘_rand’, possibly from ‘rand’ (C)
Object: ‘nem_rnd.o’
Found ‘_srand’, possibly from ‘srand’ (C)
Objects: ‘Rnem_exe.o’, ‘nem_rnd.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
* 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-3.5-bioc/meat/MANOR.Rcheck/00check.log’
for details.
* installing *source* package ‘MANOR’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c Rnem_arg.c -o Rnem_arg.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c Rnem_exe.c -o Rnem_exe.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c exememo.c -o exememo.o
exememo.c:40:13: warning: variable 'msg' is uninitialized when used here [-Wuninitialized]
sprintf(msg, "Fatal: in %s, no memory for %s (%ld elements size %ld)\n",
^˜˜
/usr/include/secure/_stdio.h:47:28: note: expanded from macro 'sprintf'
__builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
^˜˜
exememo.c:39:14: note: initialize the variable 'msg' to silence this warning
char* msg;
^
= NULL
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c nem_alg.c -o nem_alg.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c nem_hlp.c -o nem_hlp.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c nem_mod.c -o nem_mod.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c nem_nei.c -o nem_nei.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c nem_rnd.c -o nem_rnd.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c nem_ver.c -o nem_ver.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 MANOR.so Rnem_arg.o Rnem_exe.o exememo.o nem_alg.o nem_hlp.o nem_mod.o nem_nei.o nem_rnd.o nem_ver.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-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)