maanova 1.30.0
Keith Sheppard
| Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/maanova | | Last Changed Rev: 75263 / Revision: 76155 | | Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | WARNINGS | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | WARNINGS | OK |
| pelham | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | [ WARNINGS ] | OK |
* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/maanova.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'maanova/DESCRIPTION' ... OK
* this is package 'maanova' version '1.30.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'Rmpi'
* 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 'maanova' can be installed ... [5s/6s] OK
* checking installed package size ... OK
* checking package 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... WARNING
Foreign function calls with 'PACKAGE' argument in a base package:
.Call("La_svd", ..., PACKAGE = "base")
.Call("La_svd_cmplx", ..., PACKAGE = "base")
Packages should not make .C/.Call/.Fortran calls to base packages. They
are not part of the API, for use only by R itself and subject to change
without notice.
* checking R code for possible problems ... NOTE
arrayview: warning in rgb(r = r[i], g = g[i], b = b[i]): partial
argument match of 'r' to 'red'
arrayview: warning in rgb(r = r[i], g = g[i], b = b[i]): partial
argument match of 'g' to 'green'
arrayview: warning in rgb(r = r[i], g = g[i], b = b[i]): partial
argument match of 'b' to 'blue'
* 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 compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
'MPI.tex', 'Rtour.tex', 'abf1.tex', 'algorithm.tex', 'camda.tex',
'faq.tex', 'intro.tex', 'paigen.tex', 'prepfile.tex'
Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... [4s/4s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
'/Users/biocbuild/bbs-2.12-bioc/meat/maanova.Rcheck/00check.log'
for details.
* installing *source* package 'maanova' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c makeratio.c -o makeratio.o
makeratio.c:31:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp = (double *)R_alloc((*nrow)*(*ncol), sizeof(double));
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c masvd.c -o masvd.o
masvd.c:37:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
xvals = (double *) R_alloc(n * p, sizeof(double));
˜˜˜˜˜˜˜ ˜˜^˜˜
masvd.c:53:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
work = (double *) R_alloc(lwork, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜
masvd.c:64:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
int *iwork= (int *) R_alloc(8*(n<p ? n : p), sizeof(int));
˜˜˜˜˜˜˜ ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
masvd.c:76:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
work = (double *) R_alloc(lwork, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜
masvd.c:114:2: warning: '/*' within block comment [-Wcomment]
/* work on a copy of x */
^
masvd.c:154:1: warning: '/*' within block comment [-Wcomment]
/*#ifndef IEEE_754
^
masvd.c:161:5: warning: '/*' within block comment [-Wcomment]
/* work on a copy of x */
^
masvd.c:165:2: warning: '/*' within block comment [-Wcomment]
/* ask for optimal size of work array */
^
masvd.c:189:2: warning: '/*' within block comment [-Wcomment]
/* ask for optimal size of work array */
^
9 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c shift.c -o shift.o
shift.c:31:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
x = (double *)R_alloc(3*(*nrows), sizeof(double));
˜˜˜˜˜˜˜ ˜^˜˜˜˜˜˜˜˜
shift.c:48:25: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
sad[i] += abs(x[j]-med);
˜˜˜ ˜˜˜˜^˜˜˜
shift.c:27:13: warning: unused variable 'k' [-Wunused-variable]
int i, j, k;
^
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c util.c -o util.o
util.c:32:32: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
y[i] = n * unif_rand() + 1;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
util.c:45:15: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
j = n * unif_rand();
˜ ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
2 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o maanova.so makeratio.o masvd.o shift.o util.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/maanova.Rcheck/maanova/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (maanova)