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rafalab / bumphunter

bumphunter
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error loading package #2

Closed radivot closed 9 years ago

radivot commented 9 years ago

I'm getting this: library(bumphunter) Error : object ‘seqnames’ is not exported by 'namespace:GenomeInfoDb' Error: package or namespace load failed for ‘bumphunter’

version _
platform x86_64-apple-darwin13.4.0
arch x86_64
os darwin13.4.0
system x86_64, darwin13.4.0
status
major 3
minor 1.2
year 2014
month 10
day 31
svn rev 66913
language R
version.string R version 3.1.2 (2014-10-31) nickname Pumpkin Helmet

kasperdanielhansen commented 9 years ago

What is the output of biocValid()?

Kasper

On Wed, Nov 12, 2014 at 3:29 PM, Tomas Radivoyevitch < notifications@github.com> wrote:

I'm getting this: library(bumphunter) Error : object ‘seqnames’ is not exported by 'namespace:GenomeInfoDb' Error: package or namespace load failed for ‘bumphunter’

version _

platform x86_64-apple-darwin13.4.0

arch x86_64

os darwin13.4.0

system x86_64, darwin13.4.0

status

major 3

minor 1.2

year 2014

month 10

day 31

svn rev 66913

language R

version.string R version 3.1.2 (2014-10-31) nickname Pumpkin Helmet

— Reply to this email directly or view it on GitHub https://github.com/ririzarr/bumphunter/issues/2.

radivot commented 9 years ago

biocValid(bumphunter) Error in biocValid(bumphunter) : object 'bumphunter' not found

On Wed, Nov 12, 2014 at 4:07 PM, Kasper Daniel Hansen < notifications@github.com> wrote:

What is the output of biocValid()?

Kasper

On Wed, Nov 12, 2014 at 3:29 PM, Tomas Radivoyevitch < notifications@github.com> wrote:

I'm getting this: library(bumphunter) Error : object ‘seqnames’ is not exported by 'namespace:GenomeInfoDb' Error: package or namespace load failed for ‘bumphunter’

version _

platform x86_64-apple-darwin13.4.0

arch x86_64

os darwin13.4.0

system x86_64, darwin13.4.0

status

major 3

minor 1.2

year 2014

month 10

day 31

svn rev 66913

language R

version.string R version 3.1.2 (2014-10-31) nickname Pumpkin Helmet

— Reply to this email directly or view it on GitHub https://github.com/ririzarr/bumphunter/issues/2.

— Reply to this email directly or view it on GitHub https://github.com/ririzarr/bumphunter/issues/2#issuecomment-62793633.

kasperdanielhansen commented 9 years ago

No, try just

source("http://www.bioconductor.org/biocLite.R") biocValid()

I think you may have a package mismatch issue.

On Wed, Nov 12, 2014 at 5:00 PM, Tomas Radivoyevitch < notifications@github.com> wrote:

biocValid(bumphunter) Error in biocValid(bumphunter) : object 'bumphunter' not found

On Wed, Nov 12, 2014 at 4:07 PM, Kasper Daniel Hansen < notifications@github.com> wrote:

What is the output of biocValid()?

Kasper

On Wed, Nov 12, 2014 at 3:29 PM, Tomas Radivoyevitch < notifications@github.com> wrote:

I'm getting this: library(bumphunter) Error : object ‘seqnames’ is not exported by 'namespace:GenomeInfoDb' Error: package or namespace load failed for ‘bumphunter’

version _

platform x86_64-apple-darwin13.4.0

arch x86_64

os darwin13.4.0

system x86_64, darwin13.4.0

status

major 3

minor 1.2

year 2014

month 10

day 31

svn rev 66913

language R

version.string R version 3.1.2 (2014-10-31) nickname Pumpkin Helmet

— Reply to this email directly or view it on GitHub https://github.com/ririzarr/bumphunter/issues/2.

— Reply to this email directly or view it on GitHub https://github.com/ririzarr/bumphunter/issues/2#issuecomment-62793633.

— Reply to this email directly or view it on GitHub https://github.com/ririzarr/bumphunter/issues/2#issuecomment-62802751.

radivot commented 9 years ago

OK, thanks, I see a few too old and a few too new.

tom

R version 3.1.2 (2014-10-31) Platform: x86_64-apple-darwin13.4.0 (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] stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages: [1] devtools_1.6.1 locfit_1.5-9.1 iterators_1.0.7 [4] foreach_1.4.2 Biostrings_2.34.0 XVector_0.6.0 [7] S4Vectors_0.4.0 lattice_0.20-29 BiocInstaller_1.16.1 [10] ggplot2_1.0.0 reshape2_1.4 dplyr_0.3.0.2 [13] XLConnect_0.2-9 XLConnectJars_0.2-9 GenomicRanges_1.18.1 [16] IRanges_2.0.0 IlluminaHumanMethylation450kprobe_2.0.6 AnnotationDbi_1.28.1

[19] GenomeInfoDb_1.2.2 Biobase_2.26.0 BiocGenerics_0.12.0

loaded via a namespace (and not attached): [1] assertthat_0.1 codetools_0.2-9 colorspace_1.2-4 DBI_0.3.1 digest_0.6.4 doRNG_1.6 [7] grid_3.1.2 gtable_0.1.2 httr_0.5 labeling_0.3 lazyeval_0.1.9 magrittr_1.0.1 [13] MASS_7.3-35 matrixStats_0.10.3 munsell_0.4.2 pkgmaker_0.22 plyr_1.8.1 proto_0.3-10 [19] R.methodsS3_1.6.1 Rcpp_0.11.3 RCurl_1.95-4.3 registry_0.2 rJava_0.9-6 rngtools_1.2.4 [25] RSQLite_1.0.0 scales_0.2.4 stringr_0.6.2 tools_3.1.2 xtable_1.7-4 zlibbioc_1.12.0

IlluminaHumanMethylation450kprobe "2.0.6" " http://bioconductor.org/packages/3.0/data/annotation/bin/macosx/mavericks/contrib/3.1 " SNPlocs.Hsapiens.dbSNP.20110815 "0.99.6" " http://bioconductor.org/packages/3.0/data/annotation/bin/macosx/mavericks/contrib/3.1 "

update with biocLite()

downgrade with biocLite(c("bumphunter", "Rcpp", "SEERaBomb"))

Error: 2 package(s) out of date; 3 package(s) too new

On Wed, Nov 12, 2014 at 7:55 PM, Kasper Daniel Hansen < notifications@github.com> wrote:

No, try just

source("http://www.bioconductor.org/biocLite.R") biocValid()

I think you may have a package mismatch issue.

On Wed, Nov 12, 2014 at 5:00 PM, Tomas Radivoyevitch < notifications@github.com> wrote:

biocValid(bumphunter) Error in biocValid(bumphunter) : object 'bumphunter' not found

On Wed, Nov 12, 2014 at 4:07 PM, Kasper Daniel Hansen < notifications@github.com> wrote:

What is the output of biocValid()?

Kasper

On Wed, Nov 12, 2014 at 3:29 PM, Tomas Radivoyevitch < notifications@github.com> wrote:

I'm getting this: library(bumphunter) Error : object ‘seqnames’ is not exported by 'namespace:GenomeInfoDb' Error: package or namespace load failed for ‘bumphunter’

version _

platform x86_64-apple-darwin13.4.0

arch x86_64

os darwin13.4.0

system x86_64, darwin13.4.0

status

major 3

minor 1.2

year 2014

month 10

day 31

svn rev 66913

language R

version.string R version 3.1.2 (2014-10-31) nickname Pumpkin Helmet

— Reply to this email directly or view it on GitHub https://github.com/ririzarr/bumphunter/issues/2.

— Reply to this email directly or view it on GitHub https://github.com/ririzarr/bumphunter/issues/2#issuecomment-62793633.

— Reply to this email directly or view it on GitHub https://github.com/ririzarr/bumphunter/issues/2#issuecomment-62802751.

— Reply to this email directly or view it on GitHub https://github.com/ririzarr/bumphunter/issues/2#issuecomment-62823559.

radivot commented 9 years ago

it works now, thanks a bunch for telling me about biocValid

On Wed, Nov 12, 2014 at 10:11 PM, Tom Radivoyevitch radivot@gmail.com wrote:

OK, thanks, I see a few too old and a few too new.

tom

  • sessionInfo()

R version 3.1.2 (2014-10-31) Platform: x86_64-apple-darwin13.4.0 (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] stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages: [1] devtools_1.6.1 locfit_1.5-9.1 iterators_1.0.7 [4] foreach_1.4.2 Biostrings_2.34.0 XVector_0.6.0 [7] S4Vectors_0.4.0 lattice_0.20-29 BiocInstaller_1.16.1 [10] ggplot2_1.0.0 reshape2_1.4 dplyr_0.3.0.2 [13] XLConnect_0.2-9 XLConnectJars_0.2-9 GenomicRanges_1.18.1 [16] IRanges_2.0.0 IlluminaHumanMethylation450kprobe_2.0.6 AnnotationDbi_1.28.1

[19] GenomeInfoDb_1.2.2 Biobase_2.26.0 BiocGenerics_0.12.0

loaded via a namespace (and not attached): [1] assertthat_0.1 codetools_0.2-9 colorspace_1.2-4 DBI_0.3.1 digest_0.6.4 doRNG_1.6 [7] grid_3.1.2 gtable_0.1.2 httr_0.5 labeling_0.3 lazyeval_0.1.9 magrittr_1.0.1 [13] MASS_7.3-35 matrixStats_0.10.3 munsell_0.4.2 pkgmaker_0.22 plyr_1.8.1 proto_0.3-10 [19] R.methodsS3_1.6.1 Rcpp_0.11.3 RCurl_1.95-4.3 registry_0.2 rJava_0.9-6 rngtools_1.2.4 [25] RSQLite_1.0.0 scales_0.2.4 stringr_0.6.2 tools_3.1.2 xtable_1.7-4 zlibbioc_1.12.0

  • Out-of-date packages Package LibPath Installed Built IlluminaHumanMethylation450kprobe "IlluminaHumanMethylation450kprobe" "/Users/radivot/Library/R/3.1/library" "2.0.6" "3.0.0" SNPlocs.Hsapiens.dbSNP.20110815 "SNPlocs.Hsapiens.dbSNP.20110815" "/Users/radivot/Library/R/3.1/library" "0.99.6" "3.0.0" ReposVer Repository

IlluminaHumanMethylation450kprobe "2.0.6" " http://bioconductor.org/packages/3.0/data/annotation/bin/macosx/mavericks/contrib/3.1 " SNPlocs.Hsapiens.dbSNP.20110815 "0.99.6" " http://bioconductor.org/packages/3.0/data/annotation/bin/macosx/mavericks/contrib/3.1 "

update with biocLite()

  • Packages too new for Bioconductor version '3.0'

     Version     LibPath

    bumphunter "1.7.0" "/Users/radivot/Library/R/3.1/library" Rcpp "0.11.3.1" "/Users/radivot/Library/R/3.1/library" SEERaBomb "2014.10.1" "/Users/radivot/Library/R/3.1/library"

downgrade with biocLite(c("bumphunter", "Rcpp", "SEERaBomb"))

Error: 2 package(s) out of date; 3 package(s) too new

On Wed, Nov 12, 2014 at 7:55 PM, Kasper Daniel Hansen < notifications@github.com> wrote:

No, try just

source("http://www.bioconductor.org/biocLite.R") biocValid()

I think you may have a package mismatch issue.

On Wed, Nov 12, 2014 at 5:00 PM, Tomas Radivoyevitch < notifications@github.com> wrote:

biocValid(bumphunter) Error in biocValid(bumphunter) : object 'bumphunter' not found

On Wed, Nov 12, 2014 at 4:07 PM, Kasper Daniel Hansen < notifications@github.com> wrote:

What is the output of biocValid()?

Kasper

On Wed, Nov 12, 2014 at 3:29 PM, Tomas Radivoyevitch < notifications@github.com> wrote:

I'm getting this: library(bumphunter) Error : object ‘seqnames’ is not exported by 'namespace:GenomeInfoDb' Error: package or namespace load failed for ‘bumphunter’

version _

platform x86_64-apple-darwin13.4.0

arch x86_64

os darwin13.4.0

system x86_64, darwin13.4.0

status

major 3

minor 1.2

year 2014

month 10

day 31

svn rev 66913

language R

version.string R version 3.1.2 (2014-10-31) nickname Pumpkin Helmet

— Reply to this email directly or view it on GitHub https://github.com/ririzarr/bumphunter/issues/2.

— Reply to this email directly or view it on GitHub < https://github.com/ririzarr/bumphunter/issues/2#issuecomment-62793633>.

— Reply to this email directly or view it on GitHub https://github.com/ririzarr/bumphunter/issues/2#issuecomment-62802751.

— Reply to this email directly or view it on GitHub https://github.com/ririzarr/bumphunter/issues/2#issuecomment-62823559.