Hi Jianhong,
On 12/13/2013 11:45 AM, Ou, Jianhong wrote:
Dear all,
When I try to renew Rsamtools, GenomicAlignments and rtracklayer, I got error
Error : objects ‘GAlignments’, ‘GAlignmentPairs’ are not exported by
'namespace:GenomicRanges'
You didn't show us what you did exactly.
Try to do:
biocLite("GenomicRanges")
biocLite("Rsamtools")
biocLite("GenomicAlignments")
biocLite("rtracklayer")
biocLite()
in *that* order.
Cheers,
H.
Does anybody know how to figure out this problem?
biocValid()
* sessionInfo()
R Under development (unstable) (2013-09-29 r64014)
Platform: x86_64-apple-darwin12.5.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.13.3
TxDb.Mmusculus.UCSC.mm10.knownGene_2.10.1
[3] GenomicFeatures_1.15.4 AnnotationDbi_1.25.9
[5] Biobase_2.23.3 GenomicRanges_1.15.13
[7] XVector_0.3.3 IRanges_1.21.14
[9] BiocGenerics_0.9.1
loaded via a namespace (and not attached):
[1] biomaRt_2.19.1 Biostrings_2.31.3 bitops_1.0-6
[4] BSgenome_1.31.7 DBI_0.2-7 GenomicAlignments_0.99.3
[7] RCurl_1.95-4.1 Rsamtools_1.15.9 RSQLite_0.11.4
[10] rtracklayer_1.23.3 stats4_3.1.0 tools_3.1.0
[13] XML_3.98-1.1 zlibbioc_1.9.0
* Out-of-date packages
Package
GenomicAlignments "GenomicAlignments"
Rsamtools "Rsamtools"
rtracklayer "rtracklayer"
LibPath
Installed Built
GenomicAlignments "/Library/Frameworks/R.framework/Versions/3.1/Resources/library"
"0.99.3" "3.1.0"
Rsamtools "/Library/Frameworks/R.framework/Versions/3.1/Resources/library"
"1.15.9" "3.1.0"
rtracklayer "/Library/Frameworks/R.framework/Versions/3.1/Resources/library"
"1.23.3" "3.1.0"
ReposVer Repository
GenomicAlignments "0.99.9"
"http://bioconductor.org/packages/2.14/bioc/src/contrib";
Rsamtools "1.15.15"
"http://bioconductor.org/packages/2.14/bioc/src/contrib";
rtracklayer "1.23.6"
"http://bioconductor.org/packages/2.14/bioc/src/contrib";
update with biocLite()
Error: 3 package(s) out of date
Yours sincerely,
Jianhong Ou
LRB 670A
Program in Gene Function and Expression
364 Plantation Street Worcester,
MA 01605
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Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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