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lcolladotor / derfinder

Annotation-agnostic differential expression analysis of RNA-seq data via expressed regions-level or single base-level approaches
http://lcolladotor.github.io/derfinder
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doesn't load on R 3.3 #37

Closed andrewejaffe closed 7 years ago

andrewejaffe commented 7 years ago

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 7 years ago

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 7 years ago

You can also try running:

source("https://bioconductor.org/biocLite.R")
biocValid()
lcolladotor commented 7 years ago

@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.