GGtools 3.5.19
Vince Carey
| Bioconductor Changelog | | Snapshot Date: 2009-12-07 11:32:00 -0800 (Mon, 07 Dec 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GGtools | | Last Changed Rev: 43359 / Revision: 43434 | | Last Changed Date: 2009-12-03 01:55:12 -0800 (Thu, 03 Dec 2009) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | [ ERROR ] | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | ERROR | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.6-bioc/meat/GGtools.Rcheck'
* using R version 2.11.0 Under development (unstable) (2009-11-10 r50388)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GGtools/DESCRIPTION' ... OK
* this is package 'GGtools' version '3.5.19'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GGtools' 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 whether the package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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 ... NOTE
slimCisTrans : msetup: no visible binding for '<<-' assignment to 'gs'
slimCisTrans : msetup: no visible binding for global variable 'gs'
* 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 data for non-ASCII characters ... OK
* checking examples ... ERROR
Running examples in 'GGtools-Ex.R' failed.
The error most likely occurred in:
> ### * slimCTchr2SQLite
>
> flush(stderr()); flush(stdout())
>
> ### Name: slimCTchr2SQLite
> ### Title: transform matrices of chromosome-wide cis/trans eQTL statistics
> ### to SQLite or flat text, and support extraction of minimum p per SNP,
> ### with location information
> ### Aliases: slimCTchr2SQLite slimCTchr2flat minp locreport wgtinfo2browser
> ### top4
> ### Keywords: models
>
> ### ** Examples
>
> overb = options()$verbose
> example(slimCisTrans)
slmCsT> require(multicore)
Loading required package: multicore
slmCsT> data(hmceuB36.2021)
slmCsT> td = tempdir()
slmCsT> availc = multicore:::volatile$detectedCores
slmCsT> if (availc > 2) availc=availc-1
slmCsT> usec = min(5, availc)
slmCsT> time2 = unix.time(m1 <- slimCisTrans(fmla=gs~male, smlSet=hmceuB36.2021,
slmCsT+ genes2do=1:10, ncores=usec, targdir=td))
Loading required package: org.Hs.eg.db
Loading required package: org.Hs.eg.db
Loading required package: org.Hs.eg.db
multi genome-wide snp screen result:
gene set used as response:
setName: NA
geneIds: GI_10047099-S, GI_10047103-S, GI_10047105-S (total: 3)
geneIdType: Annotation (illuminaHumanv1.db)
collectionType: Null
details: use 'details(object)'
there are 3 results.
the call was:
gwSnpTests(sym = fmla, sms = smlSet)
multi genome-wide snp screen result:
gene set used as response:
setName: NA
geneIds: GI_10047121-S, GI_10047123-S, GI_10047133-A (total: 3)
geneIdType: Annotation (illuminaHumanv1.db)
collectionType: Null
details: use 'details(object)'
there are 3 results.
the call was:
gwSnpTests(sym = fmla, sms = smlSet)
multi genome-wide snp screen result:
gene set used as response:
setName: NA
geneIds: GI_10047089-S, GI_10047091-S, GI_10047093-S, GI_10047133-I (total: 4)
geneIdType: Annotation (illuminaHumanv1.db)
collectionType: Null
details: use 'details(object)'
there are 4 results.
the call was:
gwSnpTests(sym = fmla, sms = smlSet)
slmCsT> gc()
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 2056519 109.9 4953636 264.6 4953636 264.6
Vcells 12141817 92.7 32960971 251.5 49861194 380.5
slmCsT> time1 = unix.time(m1 <- slimCisTrans(fmla=gs~male, smlSet=hmceuB36.2021,
slmCsT+ genes2do=1:10, ncores=1, targdir=td))
Loading required package: org.Hs.eg.db
multi genome-wide snp screen result:
gene set used as response:
setName: NA
geneIds: GI_10047089-S, GI_10047091-S, ..., GI_10047133-I (total: 10)
geneIdType: Annotation (illuminaHumanv1.db)
collectionType: Null
details: use 'details(object)'
there are 10 results.
the call was:
gwSnpTests(sym = fmla, sms = smlSet)
slmCsT> cat("for 2 cores, time elapsed:\n")
for 2 cores, time elapsed:
slmCsT> time2
user system elapsed
4.836 4.928 3.901
slmCsT> cat("for 1 core, time elapsed:\n")
for 1 core, time elapsed:
slmCsT> time1
user system elapsed
10.392 0.096 10.516
slmCsT> dir(td)
[1] "file17555427" "GI_10047089-S+.rda" "GI_10047099-S+.rda"
[4] "GI_10047121-S+.rda" "Rdata" "Rex39b314de"
slmCsT> od = getwd()
slmCsT> setwd(td)
slmCsT> load(dir(td)[1])
Warning: file 'file17555427' has magic number '%!PS-'
Use of save versions prior to 2 is deprecated
Error: bad restore file magic number (file may be corrupted) -- no data loaded
Execution halted
* install options are ' --no-html'
* installing *source* package 'GGtools' ...
** R
** data
** inst
** preparing package for lazy loading
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: GSEABase
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: graph
Loading required package: snpMatrix
Loading required package: survival
Loading required package: splines
Loading required package: RSQLite
Loading required package: DBI
Loading required package: IRanges
Attaching package: 'IRanges'
The following object(s) are masked from package:Biobase :
updateObject
The following object(s) are masked from package:base :
Map,
cbind,
mapply,
order,
pmax,
pmax.int,
pmin,
pmin.int,
rbind,
rep.int,
table
Attaching package: 'Biostrings'
The following object(s) are masked from package:graph :
complement
** help
*** installing help indices
** building package indices ...
* DONE (GGtools)