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CHECK report for BufferedMatrixMethods on tokay1

This page was generated on 2020-10-14 11:14:28 -0400 (Wed, 14 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BufferedMatrixMethods PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 209/1930HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BufferedMatrixMethods 1.53.0
Ben Bolstad
Snapshot Date: 2020-10-13 14:40:34 -0400 (Tue, 13 Oct 2020)
URL: https://git.bioconductor.org/packages/BufferedMatrixMethods
Branch: master
Last Commit: d7d095f
Last Changed Date: 2020-04-27 14:14:37 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BufferedMatrixMethods
Version: 1.53.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BufferedMatrixMethods.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BufferedMatrixMethods_1.53.0.tar.gz
StartedAt: 2020-10-14 02:35:26 -0400 (Wed, 14 Oct 2020)
EndedAt: 2020-10-14 02:36:04 -0400 (Wed, 14 Oct 2020)
EllapsedTime: 38.2 seconds
RetCode: 0
Status:  OK  
CheckDir: BufferedMatrixMethods.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BufferedMatrixMethods.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BufferedMatrixMethods_1.53.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/BufferedMatrixMethods.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.53.0'
* 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-3.12-bioc/R/library/BufferedMatrixMethods/libs/i386/BufferedMatrixMethods.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.12-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-3.12-bioc/meat/BufferedMatrixMethods.Rcheck/00check.log'
for details.



Installation output

BufferedMatrixMethods.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/BufferedMatrixMethods_1.53.0.tar.gz && rm -rf BufferedMatrixMethods.buildbin-libdir && mkdir BufferedMatrixMethods.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BufferedMatrixMethods.buildbin-libdir BufferedMatrixMethods_1.53.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL BufferedMatrixMethods_1.53.0.zip && rm BufferedMatrixMethods_1.53.0.tar.gz BufferedMatrixMethods_1.53.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 11290  100 11290    0     0   271k      0 --:--:-- --:--:-- --:--:--  297k

install for i386

* installing *source* package 'BufferedMatrixMethods' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BufferedMatrix/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init_package.c -o init_package.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BufferedMatrix/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
       ^~~~~~~~~~~~
At top level:
preprocess_bm.c:453:12: warning: 'min' defined but not used [-Wunused-function]
 static int min(int x1,int x2){
            ^~~
C:/rtools40/mingw32/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-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BufferedMatrix/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init_package.c -o init_package.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BufferedMatrix/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
       ^~~~~~~~~~~~
At top level:
preprocess_bm.c:453:12: warning: 'min' defined but not used [-Wunused-function]
 static int min(int x1,int x2){
            ^~~
C:/rtools40/mingw64/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-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/BufferedMatrixMethods.buildbin-libdir/BufferedMatrixMethods/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BufferedMatrixMethods' as BufferedMatrixMethods_1.53.0.zip
* DONE (BufferedMatrixMethods)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'BufferedMatrixMethods' successfully unpacked and MD5 sums checked

Tests output


Example timings