doesn't load on R 3.3
andrewejaffe opened this issue · 3 comments
andrewejaffe commented
something in VariantAnnotation broke our package :(
> library(derfinder)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/jhpce/shared/community/compiler/gcc/4.4.7/R/3.3.x/lib64/R/site-library/VariantAnnotation/libs/VariantAnnotation.so':
/jhpce/shared/community/compiler/gcc/4.4.7/R/3.3.x/lib64/R/site-library/VariantAnnotation/libs/VariantAnnotation.so: undefined symbol: gzopen64
Error: package or namespace load failed for ‘derfinder’
> sessionInfo()
R version 3.3.1 Patched (2016-09-30 r71426)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.6 (Santiago)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices datasets utils methods base
loaded via a namespace (and not attached):
[1] Rcpp_0.12.8 AnnotationDbi_1.36.0
[3] XVector_0.14.0 GenomicRanges_1.26.1
[5] BiocGenerics_0.20.0 zlibbioc_1.20.0
[7] GenomicAlignments_1.10.0 IRanges_2.8.1
[9] BiocParallel_1.8.1 BSgenome_1.42.0
[11] lattice_0.20-34 GenomeInfoDb_1.10.1
[13] tools_3.3.1 SummarizedExperiment_1.4.0
[15] parallel_3.3.1 grid_3.3.1
[17] Biobase_2.34.0 DBI_0.5-1
[19] digest_0.6.10 Matrix_1.2-7.1
[21] rtracklayer_1.34.1 S4Vectors_0.12.1
[23] bitops_1.0-6 biomaRt_2.30.0
[25] RCurl_1.95-4.8 memoise_1.0.0
[27] RSQLite_1.1 GenomicFeatures_1.26.0
[29] Biostrings_2.42.1 Rsamtools_1.26.1
[31] XML_3.98-1.5 stats4_3.3.1
>
lcolladotor commented
Hi Andrew,
I don't know what versions of VariantAnnotation you are using, but you might have to re-install it. It works with both versions 1.20.1 and 1.20.2. I also haven't seen this problem in the Bioc build reports. You can also try setting your .libPaths() argument to mine and checking if that works for you before re-installing VariantAnnotation (only as a test).
Best,
Leo
With 1.20.1
> packageVersion('VariantAnnotation')
[1] ‘1.20.1’
>
> library(derfinder)
> options(width = 120)
> devtools::session_info()
Session info -----------------------------------------------------------------------------------------------------------
setting value
version R version 3.3.1 Patched (2016-09-30 r71426)
system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
tz <NA>
date 2016-12-05
Packages ---------------------------------------------------------------------------------------------------------------
package * version date source
acepack 1.4.1 2016-10-29 CRAN (R 3.3.1)
AnnotationDbi 1.36.0 2016-11-18 Bioconductor
assertthat 0.1 2013-12-06 CRAN (R 3.3.0)
Biobase 2.34.0 2016-10-20 Bioconductor
BiocGenerics 0.20.0 2016-11-17 Bioconductor
BiocParallel 1.8.1 2016-11-17 Bioconductor
biomaRt 2.30.0 2016-10-20 Bioconductor
Biostrings 2.42.0 2016-11-18 Bioconductor
bitops 1.0-6 2013-08-17 CRAN (R 3.3.0)
BSgenome 1.42.0 2016-11-18 Bioconductor
bumphunter 1.14.0 2016-11-18 Bioconductor
cluster 2.0.4 2016-04-18 CRAN (R 3.3.1)
codetools 0.2-14 2015-07-15 CRAN (R 3.3.1)
colorout * 1.1-2 2016-07-22 Github (jalvesaq/colorout@6d84420)
colorspace 1.3-1 2016-11-18 CRAN (R 3.3.1)
data.table 1.10.0 2016-12-03 CRAN (R 3.3.1)
DBI 0.5-1 2016-09-10 CRAN (R 3.3.1)
derfinder * 1.8.0 2016-11-17 Bioconductor
derfinderHelper 1.8.0 2016-11-17 Bioconductor
devtools 1.12.0 2016-06-24 CRAN (R 3.3.1)
digest 0.6.10 2016-08-02 CRAN (R 3.3.1)
doRNG 1.6 2014-03-07 CRAN (R 3.3.0)
foreach 1.4.3 2015-10-13 CRAN (R 3.3.0)
foreign 0.8-67 2016-09-13 CRAN (R 3.3.1)
Formula 1.2-1 2015-04-07 CRAN (R 3.3.0)
GenomeInfoDb 1.10.1 2016-11-17 Bioconductor
GenomicAlignments 1.10.0 2016-11-18 Bioconductor
GenomicFeatures 1.26.0 2016-11-18 Bioconductor
GenomicFiles 1.10.3 2016-11-18 Bioconductor
GenomicRanges 1.26.1 2016-11-18 Bioconductor
ggplot2 2.2.0 2016-11-11 CRAN (R 3.3.1)
gridExtra 2.2.1 2016-02-29 CRAN (R 3.3.0)
gtable 0.2.0 2016-02-26 CRAN (R 3.3.0)
Hmisc 4.0-0 2016-11-01 CRAN (R 3.3.1)
htmlTable 1.7 2016-10-19 CRAN (R 3.3.1)
htmltools 0.3.5 2016-03-21 CRAN (R 3.3.0)
IRanges 2.8.1 2016-11-18 Bioconductor
iterators 1.0.8 2015-10-13 CRAN (R 3.3.0)
knitr 1.15.1 2016-11-22 CRAN (R 3.3.1)
lattice 0.20-34 2016-09-06 CRAN (R 3.3.1)
latticeExtra 0.6-28 2016-02-09 CRAN (R 3.3.0)
lazyeval 0.2.0 2016-06-12 CRAN (R 3.3.1)
locfit 1.5-9.1 2013-04-20 CRAN (R 3.3.0)
magrittr 1.5 2014-11-22 CRAN (R 3.3.1)
Matrix 1.2-7.1 2016-09-01 CRAN (R 3.3.1)
matrixStats 0.51.0 2016-10-09 CRAN (R 3.3.1)
memoise 1.0.0 2016-01-29 CRAN (R 3.3.0)
munsell 0.4.3 2016-02-13 CRAN (R 3.3.0)
nnet 7.3-12 2016-02-02 CRAN (R 3.3.1)
pkgmaker 0.22 2014-05-14 CRAN (R 3.3.0)
plyr 1.8.4 2016-06-08 CRAN (R 3.3.1)
qvalue 2.6.0 2016-11-17 Bioconductor
RColorBrewer 1.1-2 2014-12-07 CRAN (R 3.3.0)
Rcpp 0.12.8 2016-11-17 CRAN (R 3.3.1)
RCurl 1.95-4.8 2016-03-01 CRAN (R 3.3.0)
registry 0.3 2015-07-08 CRAN (R 3.3.0)
reshape2 1.4.2 2016-10-22 CRAN (R 3.3.1)
rngtools 1.2.4 2014-03-06 CRAN (R 3.3.0)
rpart 4.1-10 2015-06-29 CRAN (R 3.3.1)
Rsamtools 1.26.1 2016-11-18 Bioconductor
RSQLite 1.1 2016-11-27 CRAN (R 3.3.1)
rtracklayer 1.34.1 2016-11-18 Bioconductor
S4Vectors 0.12.0 2016-11-18 Bioconductor
scales 0.4.1 2016-11-09 CRAN (R 3.3.1)
stringi 1.1.2 2016-10-01 CRAN (R 3.3.1)
stringr 1.1.0 2016-08-19 CRAN (R 3.3.1)
SummarizedExperiment 1.4.0 2016-11-18 Bioconductor
survival 2.40-1 2016-10-30 CRAN (R 3.3.1)
tibble 1.2 2016-08-26 CRAN (R 3.3.1)
VariantAnnotation 1.20.1 2016-11-18 Bioconductor
withr 1.0.2 2016-06-20 CRAN (R 3.3.1)
XML 3.98-1.5 2016-11-10 CRAN (R 3.3.1)
xtable 1.8-2 2016-02-05 CRAN (R 3.3.0)
XVector 0.14.0 2016-11-18 Bioconductor
zlibbioc 1.20.0 2016-10-20 Bioconductor
>With 1.20.2
> packageVersion('VariantAnnotation')
[1] ‘1.20.2’
> library('derfinder')
> options(width = 120)
> devtools::session_info()
Session info -----------------------------------------------------------------------------------------------------------
setting value
version R version 3.3.1 Patched (2016-09-30 r71426)
system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
tz <NA>
date 2016-12-05
Packages ---------------------------------------------------------------------------------------------------------------
package * version date source
acepack 1.4.1 2016-10-29 CRAN (R 3.3.1)
AnnotationDbi 1.36.0 2016-11-18 Bioconductor
assertthat 0.1 2013-12-06 CRAN (R 3.3.0)
Biobase 2.34.0 2016-10-20 Bioconductor
BiocGenerics 0.20.0 2016-11-17 Bioconductor
BiocParallel 1.8.1 2016-11-17 Bioconductor
biomaRt 2.30.0 2016-10-20 Bioconductor
Biostrings 2.42.1 2016-12-05 Bioconductor
bitops 1.0-6 2013-08-17 CRAN (R 3.3.0)
BSgenome 1.42.0 2016-11-18 Bioconductor
bumphunter 1.14.0 2016-11-18 Bioconductor
cluster 2.0.4 2016-04-18 CRAN (R 3.3.1)
codetools 0.2-14 2015-07-15 CRAN (R 3.3.1)
colorout * 1.1-2 2016-07-22 Github (jalvesaq/colorout@6d84420)
colorspace 1.3-1 2016-11-18 CRAN (R 3.3.1)
data.table 1.10.0 2016-12-03 CRAN (R 3.3.1)
DBI 0.5-1 2016-09-10 CRAN (R 3.3.1)
derfinder * 1.8.0 2016-11-17 Bioconductor
derfinderHelper 1.8.0 2016-11-17 Bioconductor
devtools 1.12.0 2016-06-24 CRAN (R 3.3.1)
digest 0.6.10 2016-08-02 CRAN (R 3.3.1)
doRNG 1.6 2014-03-07 CRAN (R 3.3.0)
foreach 1.4.3 2015-10-13 CRAN (R 3.3.0)
foreign 0.8-67 2016-09-13 CRAN (R 3.3.1)
Formula 1.2-1 2015-04-07 CRAN (R 3.3.0)
GenomeInfoDb 1.10.1 2016-11-17 Bioconductor
GenomicAlignments 1.10.0 2016-11-18 Bioconductor
GenomicFeatures 1.26.0 2016-11-18 Bioconductor
GenomicFiles 1.10.3 2016-11-18 Bioconductor
GenomicRanges 1.26.1 2016-11-18 Bioconductor
ggplot2 2.2.0 2016-11-11 CRAN (R 3.3.1)
gridExtra 2.2.1 2016-02-29 CRAN (R 3.3.0)
gtable 0.2.0 2016-02-26 CRAN (R 3.3.0)
Hmisc 4.0-0 2016-11-01 CRAN (R 3.3.1)
htmlTable 1.7 2016-10-19 CRAN (R 3.3.1)
htmltools 0.3.5 2016-03-21 CRAN (R 3.3.0)
IRanges 2.8.1 2016-11-18 Bioconductor
iterators 1.0.8 2015-10-13 CRAN (R 3.3.0)
knitr 1.15.1 2016-11-22 CRAN (R 3.3.1)
lattice 0.20-34 2016-09-06 CRAN (R 3.3.1)
latticeExtra 0.6-28 2016-02-09 CRAN (R 3.3.0)
lazyeval 0.2.0 2016-06-12 CRAN (R 3.3.1)
locfit 1.5-9.1 2013-04-20 CRAN (R 3.3.0)
magrittr 1.5 2014-11-22 CRAN (R 3.3.1)
Matrix 1.2-7.1 2016-09-01 CRAN (R 3.3.1)
matrixStats 0.51.0 2016-10-09 CRAN (R 3.3.1)
memoise 1.0.0 2016-01-29 CRAN (R 3.3.0)
munsell 0.4.3 2016-02-13 CRAN (R 3.3.0)
nnet 7.3-12 2016-02-02 CRAN (R 3.3.1)
pkgmaker 0.22 2014-05-14 CRAN (R 3.3.0)
plyr 1.8.4 2016-06-08 CRAN (R 3.3.1)
qvalue 2.6.0 2016-11-17 Bioconductor
RColorBrewer 1.1-2 2014-12-07 CRAN (R 3.3.0)
Rcpp 0.12.8 2016-11-17 CRAN (R 3.3.1)
RCurl 1.95-4.8 2016-03-01 CRAN (R 3.3.0)
registry 0.3 2015-07-08 CRAN (R 3.3.0)
reshape2 1.4.2 2016-10-22 CRAN (R 3.3.1)
rngtools 1.2.4 2014-03-06 CRAN (R 3.3.0)
rpart 4.1-10 2015-06-29 CRAN (R 3.3.1)
Rsamtools 1.26.1 2016-11-18 Bioconductor
RSQLite 1.1 2016-11-27 CRAN (R 3.3.1)
rtracklayer 1.34.1 2016-11-18 Bioconductor
S4Vectors 0.12.1 2016-12-05 Bioconductor
scales 0.4.1 2016-11-09 CRAN (R 3.3.1)
stringi 1.1.2 2016-10-01 CRAN (R 3.3.1)
stringr 1.1.0 2016-08-19 CRAN (R 3.3.1)
SummarizedExperiment 1.4.0 2016-11-18 Bioconductor
survival 2.40-1 2016-10-30 CRAN (R 3.3.1)
tibble 1.2 2016-08-26 CRAN (R 3.3.1)
VariantAnnotation 1.20.2 2016-12-05 Bioconductor
withr 1.0.2 2016-06-20 CRAN (R 3.3.1)
XML 3.98-1.5 2016-11-10 CRAN (R 3.3.1)
xtable 1.8-2 2016-02-05 CRAN (R 3.3.0)
XVector 0.14.0 2016-11-18 Bioconductor
zlibbioc 1.20.0 2016-10-20 Bioconductor
> .libPaths()
[1] "/users/lcollado/R/x86_64-pc-linux-gnu-library/3.3.x"
[2] "/jhpce/shared/community/compiler/gcc/4.4.7/R/3.3.x/lib64/R/site-library"
[3] "/jhpce/shared/community/compiler/gcc/4.4.7/R/3.3.x/lib64/R/library"lcolladotor commented
You can also try running:
source("https://bioconductor.org/biocLite.R")
biocValid()lcolladotor commented
@emilyburke just had the same issue with VariantAnnotation 1.20.2 and we fixed it by running
source("https://bioconductor.org/biocLite.R")
biocLite('VariantAnnotation')The system version at JHPCE has a problem.