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Package 132/251HostnameOS / ArchBUILDCHECKBUILD BIN
MANOR 1.11.0
Pierre Neuvial
Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MANOR
Last Changed Rev: 27716 / Revision: 29143
Last Changed Date: 2007-10-02 18:16:39 -0700 (Tue, 02 Oct 2007)
lamb1 Linux (SUSE 10.1) / x86_64  OK  ERROR 
wilson2 Linux (openSUSE 10.3) / x86_64  OK  ERROR 
wellington Linux (openSUSE 10.3) / i686  OK [ ERROR ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  ERROR  OK 
lemming Windows Server 2003 (32-bit) / x64  OK  ERROR  OK 
Package: MANOR
Version: 1.11.0
Command: /home/biocbuild/bbs-2.2-bioc/R/bin/R CMD check MANOR_1.11.0.tar.gz
StartedAt: 2007-12-11 06:57:21 -0800 (Tue, 11 Dec 2007)
EndedAt: 2007-12-11 06:59:11 -0800 (Tue, 11 Dec 2007)
EllapsedTime: 110.2 seconds
RetCode: 1
Status: ERROR
CheckDir: MANOR.Rcheck
Warnings: NA

Command output

* checking for working latex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.2-bioc/meat/MANOR.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-12-09 r43632)
* checking for file 'MANOR/DESCRIPTION' ... OK
* this is package 'MANOR' version '1.11.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'MANOR' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated 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 ... OK
* checking Rd files ... WARNING
Rd files without 'description':
  genome.plot.Rd
  MANOR-internal.Rd
  qscore.arrayCGH.Rd
  report.plot.Rd
  sort.arrayCGH.Rd
These entries are required in an Rd file.

See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating MANOR-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'MANOR-Ex.R' failed.
The error most likely occurred in:

> ### * qscore.summary
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: qscore.summary
> ### Title: Compute quality scores for a given arrayCGH object
> ### Aliases: qscore.summary.arrayCGH qscore.summary
> 
> 
> ### ** Examples
> 
> data(qscores)
> data(spatial)
> 
> ## define a list of qscores
> qscore.list <- list(clone=clone.qscore, pct.clone=pct.clone.qscore,
+ pct.spot=pct.spot.qscore, pct.replicate=pct.replicate.qscore,
+ smoothness=smoothness.qscore, dyn.x=dyn.x.qscore, dyn.y=dyn.y.qscore,
+ var.replicate=var.replicate.qscore)
> 
> ## compute quality scores for a couple of normalized arrays
> gradient.norm$quality <- qscore.summary.arrayCGH(gradient.norm,
+ qscore.list)
Error in var(x, na.rm = na.rm) : no complete element pairs
Calls: qscore.summary.arrayCGH ... aggregate.data.frame -> lapply -> FUN -> lapply -> FUN -> sd -> var
Execution halted

MANOR.Rcheck/00install.out:

/loc/home/biocbuild/bbs-2.2-bioc/meat/MANOR.Rcheck
* Installing *source* package 'MANOR' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c exememo.c -o exememo.o
exememo.c: In function ‘GenAlloc’:
exememo.c:39: warning: format ‘%ld’ expects type ‘long int’, but argument 5 has type ‘size_t’
exememo.c:39: warning: format ‘%ld’ expects type ‘long int’, but argument 6 has type ‘size_t’
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c lib_io.c -o lib_io.o
lib_io.c: In function ‘CountLinesColumns’:
lib_io.c:354: warning: ‘maxcols’ may be used uninitialized in this function
lib_io.c:354: warning: ‘mincols’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c nem_alg.c -o nem_alg.o
nem_alg.c: In function ‘ClassifyByNemOneBeta’:
nem_alg.c:1631: warning: ‘bestbeta’ may be used uninitialized in this function
nem_alg.c:1631: note: ‘bestbeta’ was declared here
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c nem_hlp.c -o nem_hlp.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c nem_mod.c -o nem_mod.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c nem_nei.c -o nem_nei.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c nem_rnd.c -o nem_rnd.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c nem_ver.c -o nem_ver.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c Rnem_arg.c -o Rnem_arg.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c Rnem_exe.c -o Rnem_exe.o
gcc -std=gnu99 -shared -L/usr/local/lib -o MANOR.so exememo.o lib_io.o nem_alg.o nem_hlp.o nem_mod.o nem_nei.o nem_rnd.o nem_ver.o Rnem_arg.o Rnem_exe.o   -L/home/biocbuild/bbs-2.2-bioc/R/lib -lR
** R
** data
** inst
** preparing package for lazy loading
Loading required package: GLAD
Loading required package: aws
Loading required package: tcltk
Loading Tcl/Tk interface ... done
[1] "Have fun with GLAD"
** help
Note: removing empty section \description
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
Note: removing empty section \description
Note: ignoring empty \keyword entries
Note: removing empty section \examples
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
Note: removing empty section \details
Note: removing empty section \examples
Note: ignoring empty \keyword entries
Note: removing empty section \details
Note: removing empty section \description
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
Note: removing empty section \description
Note: ignoring empty \keyword entries
Note: removing empty section \details
Note: removing empty section \description
 >>> Building/Updating help pages for package 'MANOR'
     Formats: text html latex example 
  MANOR-internal                    text    html    latex
  arrayTrend                        text    html    latex   example
  detectSB                          text    html    latex   example
  flag                              text    html    latex   example
  flag.arrayCGH                     text    html    latex   example
  flag.summary                      text    html    latex   example
  flags                             text    html    latex   example
  genome.plot                       text    html    latex   example
  html.report                       text    html    latex
  import                            text    html    latex   example
  nem                               text    html    latex   example
  norm.arrayCGH                     text    html    latex   example
  qscore                            text    html    latex
  qscore.arrayCGH                   text    html    latex   example
  qscore.summary                    text    html    latex   example
  qscores                           text    html    latex   example
  report.plot                       text    html    latex   example
  sort.arrayCGH                     text    html    latex   example
  spatial                           text    html    latex   example
** building package indices ...
* DONE (MANOR)