metaArray 1.55.0
Hyungwon Choi
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metaArray | | Last Changed Rev: 129129 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings metaArray_1.55.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/metaArray.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metaArray/DESCRIPTION’ ... OK
* this is package ‘metaArray’ version ‘1.55.0’
* 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 ‘metaArray’ 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 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 ... NOTE
poe.mcmc: no visible binding for global variable ‘R0’
Undefined global functions or variables:
R0
* checking Rd files ... NOTE
prepare_Rd: em.draw.Rd:28-30: Dropping empty section \examples
prepare_Rd: find.init.Rd:20-21: Dropping empty section \examples
prepare_Rd: fit.em.Rd:31-33: Dropping empty section \examples
prepare_Rd: poe.em.Rd:22: Dropping empty section \examples
* 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 compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘metaArray/libs/metaArray.so’:
Found ‘rand’, possibly from ‘rand’ (C)
Object: ‘perm.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 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: 4 NOTEs
See
‘/home/biocbuild/bbs-3.6-bioc/meat/metaArray.Rcheck/00check.log’
for details.
* installing *source* package ‘metaArray’ ...
** libs
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -DUSEDOUBLE -fpic -g -O2 -Wall -c contr.c -o contr.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -DUSEDOUBLE -fpic -g -O2 -Wall -c dproc.c -o dproc.o
dproc.c: In function ‘malloc_CH’:
dproc.c:111:21: warning: variable ‘num’ set but not used [-Wunused-but-set-variable]
int i, j, nr, nc, num;
^
dproc.c: In function ‘free_CH’:
dproc.c:192:16: warning: unused variable ‘nc’ [-Wunused-variable]
int num, nr, nc;
^
dproc.c:192:12: warning: variable ‘nr’ set but not used [-Wunused-but-set-variable]
int num, nr, nc;
^
dproc.c:192:7: warning: variable ‘num’ set but not used [-Wunused-but-set-variable]
int num, nr, nc;
^
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -DUSEDOUBLE -fpic -g -O2 -Wall -c dproc2.c -o dproc2.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -DUSEDOUBLE -fpic -g -O2 -Wall -c intcor.c -o intcor.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -DUSEDOUBLE -fpic -g -O2 -Wall -c lowess.c -o lowess.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -DUSEDOUBLE -fpic -g -O2 -Wall -c mmath.c -o mmath.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -DUSEDOUBLE -fpic -g -O2 -Wall -c perm.c -o perm.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -DUSEDOUBLE -fpic -g -O2 -Wall -c poe.c -o poe.o
poe.c: In function ‘poe_one_iter’:
poe.c:131:53: warning: variable ‘shift’ set but not used [-Wunused-but-set-variable]
double kappa_b, kappa_a, kappa_new, aaa, res_max, shift;
^
poe.c:120:20: warning: variable ‘accept’ set but not used [-Wunused-but-set-variable]
int nr,nc,tt,gg, accept;
^
gcc -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o metaArray.so contr.o dproc.o dproc2.o intcor.o lowess.o mmath.o perm.o poe.o -lm -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/metaArray.Rcheck/metaArray/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 (metaArray)