Dear all,

When I try to renew Rsamtools, GenomicAlignments and rtracklayer, I got error

Error : objects ‘GAlignments’, ‘GAlignmentPairs’ are not exported by 'namespace:GenomicRanges'

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* Out-of-date packages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Error: 3 package(s) out of date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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