rnaSeqMap 2.14.0
Michal Okoniewski
| 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/rnaSeqMap | | 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 | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | N O T S U P P O R T E D |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
| pelham | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | [ OK ] | OK |
* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/rnaSeqMap.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 'rnaSeqMap/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rnaSeqMap' version '2.14.0'
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'rnaSeqMap' can be installed ... [29s/30s] 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 ... OK
* checking R code for possible problems ... NOTE
qq_derivative_plot: warning in qqplot(dd[, 1], dd[, 2], , plot = F):
partial argument match of 'plot' to 'plot.it'
qq_plot: warning in qqplot(dd[, 1], dd[, 2], , plot = F): partial
argument match of 'plot' to 'plot.it'
bam2sig: no visible global function definition for 'dbGetQuery'
* 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 examples ... [16s/16s] 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
NOTE: There were 2 notes.
See
'/Users/biocbuild/bbs-2.12-bioc/meat/rnaSeqMap.Rcheck/00check.log'
for details.
* installing *source* package 'rnaSeqMap' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c Rinit.c -o Rinit.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c gcoverage.c -o gcoverage.o
gcoverage.c:21:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
xwyn = (int *) R_alloc(nwyn, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜
gcoverage.c:33:50: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(INTEGER(wyn), xwyn, sizeof(int) * nwyn);
˜ ^˜˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
gcoverage.c:33:50: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(INTEGER(wyn), xwyn, sizeof(int) * nwyn);
˜ ^˜˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
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 ghistogram.c -o ghistogram.o
ghistogram.c:22:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
xab = (int *) R_alloc(nab, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜
ghistogram.c:36:41: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(INTEGER(ab), xab, sizeof(int) * nab);
˜ ^˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
ghistogram.c:36:41: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(INTEGER(ab), xab, sizeof(int) * nab);
˜ ^˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
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 regionmining.c -o regionmining.o
regionmining.c:38:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
xwyn = (int *) R_alloc(2*nwyn,sizeof(int));
˜˜˜˜˜˜˜ ˜^˜˜˜˜
regionmining.c:78:41: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(INTEGER(wyn),xwyn,sizeof(int) * j);
˜ ^
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
regionmining.c:78:41: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(INTEGER(wyn),xwyn,sizeof(int) * j);
˜ ^
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
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 splicingind.c -o splicingind.o
splicingind.c:18:11: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
con = NUMERIC_POINTER(c)[0];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rdefines.h:82:28: note: expanded from macro 'NUMERIC_POINTER'
#define NUMERIC_POINTER(x) REAL(x)
^
splicingind.c:38:14: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
si=xa[j]/(xb[j]*con);
˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
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 rnaSeqMap.so Rinit.o gcoverage.o ghistogram.o regionmining.o splicingind.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/rnaSeqMap.Rcheck/rnaSeqMap/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 (rnaSeqMap)