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BioC 3.4: CHECK report for simpleaffy on moscato1

This page was generated on 2016-09-21 03:41:16 -0700 (Wed, 21 Sep 2016).

Package 1122/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
simpleaffy 2.49.0
Crispin Miller
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/simpleaffy
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: simpleaffy
Version: 2.49.0
Command: rm -rf simpleaffy.buildbin-libdir simpleaffy.Rcheck && mkdir simpleaffy.buildbin-libdir simpleaffy.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=simpleaffy.buildbin-libdir simpleaffy_2.49.0.tar.gz >simpleaffy.Rcheck\00install.out 2>&1 && cp simpleaffy.Rcheck\00install.out simpleaffy-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=simpleaffy.buildbin-libdir --install="check:simpleaffy-install.out" --force-multiarch --no-vignettes --timings simpleaffy_2.49.0.tar.gz
StartedAt: 2016-09-20 16:42:26 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 16:45:37 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 190.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: simpleaffy.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf simpleaffy.buildbin-libdir simpleaffy.Rcheck && mkdir simpleaffy.buildbin-libdir simpleaffy.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=simpleaffy.buildbin-libdir simpleaffy_2.49.0.tar.gz >simpleaffy.Rcheck\00install.out 2>&1 && cp simpleaffy.Rcheck\00install.out simpleaffy-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=simpleaffy.buildbin-libdir --install="check:simpleaffy-install.out" --force-multiarch --no-vignettes --timings simpleaffy_2.49.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/simpleaffy.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'simpleaffy/DESCRIPTION' ... OK
* this is package 'simpleaffy' version '2.49.0'
* 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 'simpleaffy' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods' 'utils' 'grDevices' 'graphics' 'stats' 'BiocGenerics' 'Biobase' 'affy' 'genefilter' 'gcrma'
A package should be listed in only one of these fields.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
hmap.eset : <anonymous>: no visible global function definition for
  'var'
hmap.pc : <anonymous>: no visible global function definition for 'var'
qc.affy: no visible binding for global variable 'var'
standard.pearson: no visible global function definition for 'cor'
Undefined global functions or variables:
  cor var
Consider adding
  importFrom("stats", "cor", "var")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'PairComp,ANY,ANY,ANY'
  generic '[<-' and siglist 'PairComp,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.4-bioc/meat/simpleaffy.buildbin-libdir/simpleaffy/libs/i386/simpleaffy.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 the system RNG.
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/simpleaffy.Rcheck/00check.log'
for details.


simpleaffy.Rcheck/00install.out:


install for i386

* installing *source* package 'simpleaffy' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c simpleaffy.c -o simpleaffy.o
simpleaffy.c: In function 'bgmas':
simpleaffy.c:440:30: warning: passing argument 1 of 'REprintf' from incompatible pointer type
     if(gn >= ngrid) REprintf(stderr,"Really ouch! %d %d\n",gn,ends[gn]);
                              ^
In file included from D:/biocbld/BBS-3˜1.4-B/R/include/R.h:72:0,
                 from simpleaffy.c:5:
D:/biocbld/BBS-3˜1.4-B/R/include/R_ext/Print.h:40:6: note: expected 'const char *' but argument is of type 'struct FILE *'
 void REprintf(const char *, ...);
      ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o simpleaffy.dll tmp.def simpleaffy.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/simpleaffy.buildbin-libdir/simpleaffy/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'simpleaffy' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c simpleaffy.c -o simpleaffy.o
simpleaffy.c: In function 'bgmas':
simpleaffy.c:440:30: warning: passing argument 1 of 'REprintf' from incompatible pointer type
     if(gn >= ngrid) REprintf(stderr,"Really ouch! %d %d\n",gn,ends[gn]);
                              ^
In file included from D:/biocbld/BBS-3˜1.4-B/R/include/R.h:72:0,
                 from simpleaffy.c:5:
D:/biocbld/BBS-3˜1.4-B/R/include/R_ext/Print.h:40:6: note: expected 'const char *' but argument is of type 'struct FILE *'
 void REprintf(const char *, ...);
      ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o simpleaffy.dll tmp.def simpleaffy.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/simpleaffy.buildbin-libdir/simpleaffy/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'simpleaffy' as simpleaffy_2.49.0.zip
* DONE (simpleaffy)

simpleaffy.Rcheck/examples_i386/simpleaffy-Ex.timings:

nameusersystemelapsed
all.present000
all.present.in.group000
bg.correct.sa000
call.exprs000
detection.p.val000
get.annotation000
get.array.indices000
get.array.subset000
get.array.subset.affy000
get.fold.change.and.t.test000
hmap.colors000
hmap.eset000
hmap.pc000
journalpng000
justMAS000
pairwise.comparison000
pairwise.filter000
plot.pairwise.comparison000
plot.qc.stats0.060.000.06
qc0.050.020.07
qc.affy0.060.000.06
qc.get.alpha10.020.000.01
qc.get.array000
qc.get.probes000
qc.get.ratios0.010.000.02
qc.get.spikes000
qc.have.params0.020.000.01
qc.ok000
qc.read.file0.020.000.02
qc.stats0.040.000.05
read.affy000
read.affy.mixed000
setQCEnvironment000
simpleaffy-deprecated0.010.000.02
standard.pearson000
trad.scatter.plot000

simpleaffy.Rcheck/examples_x64/simpleaffy-Ex.timings:

nameusersystemelapsed
all.present000
all.present.in.group000
bg.correct.sa000
call.exprs000
detection.p.val000
get.annotation000
get.array.indices000
get.array.subset000
get.array.subset.affy000
get.fold.change.and.t.test000
hmap.colors000
hmap.eset000
hmap.pc000
journalpng000
justMAS000
pairwise.comparison000
pairwise.filter000
plot.pairwise.comparison000
plot.qc.stats0.060.010.07
qc0.050.000.05
qc.affy0.050.000.05
qc.get.alpha1000
qc.get.array000
qc.get.probes000
qc.get.ratios000
qc.get.spikes000
qc.have.params0.000.020.02
qc.ok000
qc.read.file000
qc.stats0.060.000.06
read.affy000
read.affy.mixed000
setQCEnvironment000
simpleaffy-deprecated0.020.000.02
standard.pearson000
trad.scatter.plot000