Ben Bolstad
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/BufferedMatrixMethods |
| Branch: RELEASE_3_9 |
| Last Commit: 49f5508 |
| Last Changed Date: 2019-05-02 11:53:07 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:21:04 -0400 (Wed, 16 Oct 2019).
| Package 194/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BufferedMatrixMethods 1.48.0 Ben Bolstad
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: BufferedMatrixMethods |
| Version: 1.48.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BufferedMatrixMethods.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings BufferedMatrixMethods_1.48.0.tar.gz |
| StartedAt: 2019-10-16 02:21:37 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 02:22:08 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 31.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrixMethods.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BufferedMatrixMethods.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings BufferedMatrixMethods_1.48.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/BufferedMatrixMethods.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BufferedMatrixMethods/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BufferedMatrixMethods' 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 whether package 'BufferedMatrixMethods' can be installed ... OK
* checking installed package size ... OK
* checking package 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
'library' or 'require' calls in package code:
'affy' 'affyio'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
'BufferedMatrix' 'methods'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
median.polish.summarize
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function calls to a different package:
.Call("ReadHeader", ..., PACKAGE = "affyio")
.Call("read_probeintensities", ..., PACKAGE = "affyio")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
BufferedMatrix.bg.correct.normalize.quantiles: no visible global
function definition for 'is'
BufferedMatrix.bg.correct.normalize.quantiles: no visible global
function definition for 'duplicate'
BufferedMatrix.bg.correct.normalize.quantiles : bg.dens: no visible
global function definition for 'density'
BufferedMatrix.justRMA: no visible global function definition for 'new'
BufferedMatrix.justRMA: no visible global function definition for
'pData'
BufferedMatrix.justRMA: no visible global function definition for
'read.celfile.header'
BufferedMatrix.justRMA: no visible global function definition for
'cleancdfname'
BufferedMatrix.justRMA: no visible global function definition for
'pmindex'
BufferedMatrix.justRMA: no visible global function definition for
'geneNames'
BufferedMatrix.justRMA: no visible global function definition for
'set.buffer.dim'
BufferedMatrix.justRMA: no visible global function definition for
'RowMode'
BufferedMatrix.justRMA: no visible global function definition for
'notes<-'
BufferedMatrix.read.celfiles: no visible global function definition for
'createBufferedMatrix'
BufferedMatrix.read.celfiles: no visible global function definition for
'read.celfile'
BufferedMatrix.read.celfiles: no visible global function definition for
'AddColumn'
BufferedMatrix.read.probematrix: no visible global function definition
for 'new'
BufferedMatrix.read.probematrix: no visible global function definition
for 'cleancdfname'
BufferedMatrix.read.probematrix: no visible global function definition
for 'getCdfInfo'
BufferedMatrix.read.probematrix: no visible global function definition
for 'createBufferedMatrix'
BufferedMatrix.read.probematrix: no visible global function definition
for 'AddColumn'
bg.correct.BufferedMatrix: no visible global function definition for
'is'
bg.correct.BufferedMatrix: no visible global function definition for
'duplicate'
bg.correct.BufferedMatrix : bg.dens: no visible global function
definition for 'density'
normalize.BufferedMatrix.quantiles: no visible global function
definition for 'is'
normalize.BufferedMatrix.quantiles: no visible global function
definition for 'duplicate'
Undefined global functions or variables:
AddColumn RowMode cleancdfname createBufferedMatrix density duplicate
geneNames getCdfInfo is new notes<- pData pmindex read.celfile
read.celfile.header set.buffer.dim
Consider adding
importFrom("methods", "is", "new")
importFrom("stats", "density")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/BufferedMatrixMethods/libs/i386/BufferedMatrixMethods.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/BufferedMatrixMethods/libs/x64/BufferedMatrixMethods.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking examples ... NONE
* checking PDF version of manual ... OK
* DONE
Status: 6 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/BufferedMatrixMethods.Rcheck/00check.log'
for details.
BufferedMatrixMethods.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/BufferedMatrixMethods_1.48.0.tar.gz && rm -rf BufferedMatrixMethods.buildbin-libdir && mkdir BufferedMatrixMethods.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BufferedMatrixMethods.buildbin-libdir BufferedMatrixMethods_1.48.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL BufferedMatrixMethods_1.48.0.zip && rm BufferedMatrixMethods_1.48.0.tar.gz BufferedMatrixMethods_1.48.0.zip
###
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install for i386
* installing *source* package 'BufferedMatrixMethods' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BufferedMatrix/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c init_package.c -o init_package.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BufferedMatrix/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c preprocess_bm.c -o preprocess_bm.o
preprocess_bm.c: In function 'bm_rma_bg_correct':
preprocess_bm.c:344:7: warning: unused variable 'i' [-Wunused-variable]
int i,j;
^
preprocess_bm.c: In function 'R_bm_rma_bg_correct':
preprocess_bm.c:378:7: warning: unused variable 'current_mode' [-Wunused-variable]
int current_mode;
^
preprocess_bm.c: In function 'R_bm_quantile_normalize':
preprocess_bm.c:593:7: warning: unused variable 'current_mode' [-Wunused-variable]
int current_mode;
^
preprocess_bm.c: In function 'do_RMA_buffmat':
preprocess_bm.c:924:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
int first_ind;
^
preprocess_bm.c: In function 'R_bm_rma_bg_correct_quantile_normalize':
preprocess_bm.c:1151:7: warning: unused variable 'current_mode' [-Wunused-variable]
int current_mode;
^
preprocess_bm.c: At top level:
preprocess_bm.c:453:12: warning: 'min' defined but not used [-Wunused-function]
static int min(int x1,int x2){
^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o BufferedMatrixMethods.dll tmp.def init_package.o preprocess_bm.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/BufferedMatrixMethods.buildbin-libdir/00LOCK-BufferedMatrixMethods/00new/BufferedMatrixMethods/libs/i386
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'BufferedMatrixMethods'
finding HTML links ... done
BM_affyDataInput html
BM_justRMA html
BM_readcelfiles html
rmapreprocess.bufferedmatrix html
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'BufferedMatrixMethods' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BufferedMatrix/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c init_package.c -o init_package.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BufferedMatrix/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c preprocess_bm.c -o preprocess_bm.o
preprocess_bm.c: In function 'bm_rma_bg_correct':
preprocess_bm.c:344:7: warning: unused variable 'i' [-Wunused-variable]
int i,j;
^
preprocess_bm.c: In function 'R_bm_rma_bg_correct':
preprocess_bm.c:378:7: warning: unused variable 'current_mode' [-Wunused-variable]
int current_mode;
^
preprocess_bm.c: In function 'R_bm_quantile_normalize':
preprocess_bm.c:593:7: warning: unused variable 'current_mode' [-Wunused-variable]
int current_mode;
^
preprocess_bm.c: In function 'do_RMA_buffmat':
preprocess_bm.c:924:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
int first_ind;
^
preprocess_bm.c: In function 'R_bm_rma_bg_correct_quantile_normalize':
preprocess_bm.c:1151:7: warning: unused variable 'current_mode' [-Wunused-variable]
int current_mode;
^
preprocess_bm.c: At top level:
preprocess_bm.c:453:12: warning: 'min' defined but not used [-Wunused-function]
static int min(int x1,int x2){
^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o BufferedMatrixMethods.dll tmp.def init_package.o preprocess_bm.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/BufferedMatrixMethods.buildbin-libdir/BufferedMatrixMethods/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BufferedMatrixMethods' as BufferedMatrixMethods_1.48.0.zip
* DONE (BufferedMatrixMethods)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'BufferedMatrixMethods' successfully unpacked and MD5 sums checked