BufferedMatrixMethods 1.40.0
B. M. Bolstad
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/BufferedMatrixMethods | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings BufferedMatrixMethods_1.40.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/BufferedMatrixMethods.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 ‘BufferedMatrixMethods/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BufferedMatrixMethods’ version ‘1.40.0’
* 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 ‘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
* 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 loading without being on the library search path ... 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 ... OK
* 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 ... OK
* checking examples ... NONE
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.5-bioc/meat/BufferedMatrixMethods.Rcheck/00check.log’
for details.
* installing *source* package ‘BufferedMatrixMethods’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/BufferedMatrix/include" -I/usr/local/include -fpic -g -O2 -Wall -c init_package.c -o init_package.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/BufferedMatrix/include" -I/usr/local/include -fpic -g -O2 -Wall -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){
^
gcc -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o BufferedMatrixMethods.so init_package.o preprocess_bm.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/BufferedMatrixMethods.Rcheck/BufferedMatrixMethods/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (BufferedMatrixMethods)