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 |
* 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
/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
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>>> 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)