Hello,
I'm trying to load an R package (library?) called BiSeq
, which has a web of dependencies, and when I load the library I get:
'BiocParallel' did not register default BiocParallelParams:
invalid class “MulticoreParam” object: 1: ‘cluster’, ‘.clusterargs’, ‘RNGseed’ must be length 1
invalid class “MulticoreParam” object: 2: ‘timeout’, ‘log’ must be length 1
my session information:
> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS
Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.so
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] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] BiSeq_1.10.0 Formula_1.2-2
[3] SummarizedExperiment_1.0.2 Biobase_2.30.0
[5] GenomicRanges_1.22.4 GenomeInfoDb_1.6.3
[7] IRanges_2.4.8 S4Vectors_0.8.11
[9] BiocGenerics_0.16.1
loaded via a namespace (and not attached):
[1] Rcpp_0.12.13 compiler_3.4.2 nloptr_1.0.4
[4] futile.logger_1.4.3 XVector_0.10.0 bitops_1.0-6
[7] futile.options_1.0.0 tools_3.4.2 zlibbioc_1.16.0
[10] digest_0.6.12 bit_1.1-12 lme4_1.1-14
[13] memoise_1.1.0 tibble_1.3.4 RSQLite_2.0
[16] annotate_1.48.0 nlme_3.1-131 lattice_0.20-35
[19] rlang_0.1.2 Matrix_1.2-11 DBI_0.7
[22] rtracklayer_1.30.4 Biostrings_2.38.4 bit64_0.9-7
[25] globaltest_5.24.0 lmtest_0.9-35 grid_3.4.2
[28] nnet_7.3-12 flexmix_2.3-14 AnnotationDbi_1.32.3
[31] survival_2.41-3 XML_3.98-1.9 BiocParallel_1.4.3
[34] lokern_1.1-8 minqa_1.2.4 blob_1.1.0
[37] lambda.r_1.2 GenomicAlignments_1.6.3 Rsamtools_1.22.0
[40] modeltools_0.2-21 MASS_7.3-47 splines_3.4.2
[43] sfsmisc_1.1-1 xtable_1.8-2 betareg_3.1-0
[46] sandwich_2.4-0 RCurl_1.95-4.8 zoo_1.8-0
I get a similar error on another system, but worse:
'BiocParallel' did not register default BiocParallelParams:
invalid class “MulticoreParam” object: 1: ‘cluster’, ‘.clusterargs’, ‘.uid’, ‘RNGseed’ must be length 1
invalid class “MulticoreParam” object: 2: ‘.clusterargs’, ‘.controlled’, ‘logdir’, ‘resultdir’ must be length 1
Warning message:
In is.na(x[[i]]) :
is.na() applied to non-(list or vector) of type 'environment
which has the session info:
> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS
Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.0
LAPACK: /usr/lib/lapack/liblapack.so.3.0
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] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] BiSeq_1.12.0 Formula_1.2-2
[3] SummarizedExperiment_1.2.3 Biobase_2.32.0
[5] GenomicRanges_1.24.3 GenomeInfoDb_1.8.7
[7] IRanges_2.6.1 S4Vectors_0.10.3
[9] BiocGenerics_0.18.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.13 compiler_3.4.2 XVector_0.12.1
[4] bitops_1.0-6 tools_3.4.2 zlibbioc_1.18.0
[7] digest_0.6.12 bit_1.1-12 memoise_1.1.0
[10] tibble_1.3.4 annotate_1.50.1 RSQLite_2.0
[13] lattice_0.20-35 rlang_0.1.2 Matrix_1.2-11
[16] DBI_0.7 rtracklayer_1.32.2 Biostrings_2.40.2
[19] bit64_0.9-7 lmtest_0.9-35 grid_3.4.2
[22] nnet_7.3-12 globaltest_5.26.0 flexmix_2.3-14
[25] AnnotationDbi_1.34.4 survival_2.41-3 XML_3.98-1.9
[28] BiocParallel_1.6.6 lokern_1.1-8 blob_1.1.0
[31] splines_3.4.2 Rsamtools_1.24.0 modeltools_0.2-21
[34] sfsmisc_1.1-1 GenomicAlignments_1.8.4 xtable_1.8-2
[37] betareg_3.1-0 sandwich_2.4-0 RCurl_1.95-4.8
[40] zoo_1.8-0
Googling this produces no solutions, only 1 other person has had this problem before. How can I load this BiSeq library/package correctly?
hi Kevin, my Bioconductor on the 1st computer is
my Bioconductor on the 2nd computer is
and yes, you are correct, there are no loaded packages which could be interfering. BiSeq was installed from BioConductor.
-Dave
Hi Dave, that's weird because I have the same version of Bioconductor and BiocInstaller as per your 1st computer.
Just 3 more things to try:
install.packages()
and choose a mirrorIn the past, the final option, although not ideal, has always resolved these package issues for me
hi Kevin,
thanks for your work.
1) BiocParallel is installed, and gives the same warning message that BiSeq does, which tells me that nothing may be wrong with BiSeq itself, but in one of its many many dependencies
2) BiSeq is already installed
3) this is on a computer where I don't have root privilege, I re-downloaded R and installed another copy of it, but it somehow still accesses the same libraries (which shows the same error just like the main installation will when it tries to load BiSeq)
I have also attempted to fix BiocParallel from https://support.bioconductor.org/p/95306/ but this fails as well:
Hey, I have just successfully installed and loaded this package (Ubuntu 14.04; R 3.2.5), by opening a 'brand' new session and typing:
Just to be sure, have you installed it from Bioconductor and in a new session with no loaded packages?