affy 1.38.1
Rafael A. Irizarry
| 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/affy | | Last Changed Rev: 75788 / Revision: 76155 | | Last Changed Date: 2013-04-18 14:30:32 -0700 (Thu, 18 Apr 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| 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/affy.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 'affy/DESCRIPTION' ... OK
* this is package 'affy' version '1.38.1'
* 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 'affy' can be installed ... [8s/10s] 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 ... NOTE
Foreign function calls with 'PACKAGE' argument in a different package:
.Call("read_abatch", ..., PACKAGE = "affyio")
.Call("read_abatch_stddev", ..., PACKAGE = "affyio")
See the chapter 'System and foreign language interfaces' of the
'Writing R Extensions' manual.
* checking R code for possible problems ... NOTE
featureNames,AffyBatch: warning in ls(env = cdf.envir): partial
argument match of 'env' to 'envir'
geneNames,AffyBatch: warning in ls(env = cdf.envir): partial argument
match of 'env' to 'envir'
show,AffyBatch: warning in ls(env = cdf.env): partial argument match of
'env' to 'envir'
cleancdfname: no visible binding for global variable 'mapCdfName'
* 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' ... OK
* checking examples ... [180s/210s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
mas5 57.928 0.818 60.744
MAplot 30.700 1.304 34.865
expresso 27.619 1.002 33.067
bgc 8.612 0.486 9.811
AffyBatch-class 7.908 0.264 8.430
AffyRNAdeg 6.458 0.180 6.766
maffy.normalise 3.907 0.104 5.260
ProgressBarText-class 1.438 0.115 17.446
* 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/affy.Rcheck/00check.log'
for details.
* installing *source* package 'affy' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DHAVE_ZLIB=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include" -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c chipbackground.c -o chipbackground.o
chipbackground.c:379:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
qsort(data_by_sector[j],cur_n[j],sizeof(double),(int(*)(const void*, const void*))sort_double);
˜˜˜˜˜ ^˜˜˜˜˜˜˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DHAVE_ZLIB=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include" -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c getall_locations.c -o getall_locations.o
getall_locations.c:38:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
nbElements = (int *)R_alloc(nb_affyid, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DHAVE_ZLIB=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include" -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c mas5calls.c -o mas5calls.o
mas5calls.c:96:31: warning: implicit conversion turns floating-point number into integer: 'double' to 'size_t' (aka 'unsigned long') [-Wconversion]
r = (double *) R_alloc(nx,sizeof(double));
˜˜˜˜˜˜˜ ^˜
mas5calls.c:97:31: warning: implicit conversion turns floating-point number into integer: 'double' to 'size_t' (aka 'unsigned long') [-Wconversion]
absx = (double *) R_alloc(nx,sizeof(double));
˜˜˜˜˜˜˜ ^˜
mas5calls.c:98:28: warning: implicit conversion turns floating-point number into integer: 'double' to 'size_t' (aka 'unsigned long') [-Wconversion]
xidx = (int *) R_alloc(nx,sizeof(int));
˜˜˜˜˜˜˜ ^˜
mas5calls.c:104:30: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
rsort_with_index(absx,xidx,nx);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜
mas5calls.c:105:13: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
rank(absx,nx,r);
˜˜˜˜ ^˜
mas5calls.c:151:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ignore = (int *) R_alloc(n, sizeof(int));
˜˜˜˜˜˜˜ ^
mas5calls.c:175:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
dv = (double *) R_alloc(n, sizeof(double));
˜˜˜˜˜˜˜ ^
7 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DHAVE_ZLIB=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include" -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c rma2.c -o rma2.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DHAVE_ZLIB=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include" -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c rma_common.c -o rma_common.o
rma_common.c:64:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(buffer,x,length*sizeof(double));
^˜˜˜˜˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
rma_common.c:64:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(buffer,x,length*sizeof(double));
^˜˜˜˜˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
rma_common.c:106:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(buffer,x,length*sizeof(double));
^˜˜˜˜˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
rma_common.c:106:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(buffer,x,length*sizeof(double));
^˜˜˜˜˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
4 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 affy.so chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/affy.Rcheck/affy/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
Creating a generic function for 'open' from package 'base' in package 'affy'
Creating a generic function for 'close' from package 'base' in package 'affy'
Creating a generic function for 'barplot' from package 'graphics' in package 'affy'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (affy)