Open ryao-mdanderson opened 3 years ago
schmic05
commented
3 years ago Hi @ryao-mdanderson
Could you please check, if this error also occurs with the most recent version of the package at https://github.com/MPIIComputationalEpigenetics/WSHPackage? My bad that I did not mention that the source code has been moved to another location.
Thanks for reporting and best,
Michael
ryao-mdanderson
commented
3 years ago Hi Michael,
Thank you for your reply, I tried to install the WSH package with the most recent version at https://github.com/MPIIComputationalEpigenetics/WSHPackage
The installation requires a few Bioconductor packages as well: BiocManager::install(pkgs=(c("MatrixGenerics", "GenomicRanges", "org.Hs.eg.db", "AnnotationDbi", "DelayedArray","RnBeads", "RnBeads.hg38")))
After the requirement meets, I am able to install WSH and load the package without an error.
However, I ran the example, the last command still does not work.
qfdrp <- rnb.calculate.qfdrp(example.rnb.set,example.bam) 2021-03-03 09:45:19 1.5 STATUS STARTED Computing qFDRP from RnBSet object 2021-03-03 09:46:03 5.1 STATUS STARTED Removing Sex chromosomes 2021-03-03 09:46:03 5.1 STATUS COMPLETED Removing Sex chromosomes 2021-03-03 09:46:04 5.1 STATUS STARTED qFDRP calculation Error in checkForRemoteErrors(lapply(cl, recvResult)) : one node produced an error: object '.doSnowGlobals' not found
schmic05
commented
3 years ago Hmm, that's weird. I just tried it on my machine (CentOS 7.9 with conda and R-4.0.3) and it worked just fine. Another option that you could try is to use the following to install RnBeads (the main dependency):
source("https://rnbeads.org/data/install.R")
before installing the package. Otherwise, I don't have a clue, since you did not activate the parallel processing options (or did you?)
ryao-mdanderson
commented
3 years ago Hi Michael,
I tried install RnBeads via this command:
install.packages("https://rnbeads.org/data/install.R") it outputs: Warning message: package ‘https://rnbeads.org/data/install.R’ is not available for this version of R
A version of this package for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
Any suggestion? I did not activate the parallel processing options.
Thanks! Rong
ryao-mdanderson
commented
3 years ago Hi Michael,
Somehow, the package with the example works on my another personal library R/3.6.0 (devtools already installed, so I did not install devtools).
schmic05
commented
3 years ago Hi @ryao-mdanderson
Thanks for the update. I am not really sure what the error might be and it is hard for me to track it down if I cannot reproduce the error. Sorry for the inconvenience.
PS: You should have called
source("https://rnbeads.org/data/install.R")
instead of
install.packages("https://rnbeads.org/data/install.R")
Best, Michael
ryao-mdanderson
commented
3 years ago Hi Michael,
Sorry for my late update. I create a clean R/4.0.3 personal library, use the command source("https://rnbeads.org/data/install.R")
and installed WSH followed your site https://github.com/MPIIComputationalEpigenetics/WSHPackage
the installation goes well, no error. but when I ran the example, I am still seeing
qfdrp <- rnb.calculate.qfdrp(example.rnb.set,example.bam) 2021-03-09 21:56:15 1.5 STATUS STARTED Computing qFDRP from RnBSet object 2021-03-09 21:56:55 5.1 STATUS STARTED Removing Sex chromosomes 2021-03-09 21:56:55 5.1 STATUS COMPLETED Removing Sex chromosomes 2021-03-09 21:56:55 5.1 STATUS STARTED qFDRP calculation Error in checkForRemoteErrors(lapply(cl, recvResult)) : one node produced an error: object '.doSnowGlobals' not found
You have CentOS 7.9, I am on RHEL 7.4, there might be some subtle differences that I am not awared.
I will try other R versions. Thank you very much for your helps. Rong
ryao-mdanderson
commented
3 years ago Hi Michael,
I am using R/3.6.0. The installation goes well, however, I hit a different error when running the example:
qfdrp <- rnb.calculate.qfdrp(example.rnb.set,example.bam) 2021-03-10 12:02:08 1.3 STATUS STARTED Computing qFDRP from RnBSet object 2021-03-10 12:02:51 4.8 STATUS STARTED Removing Sex chromosomes 2021-03-10 12:02:51 4.8 STATUS COMPLETED Removing Sex chromosomes 2021-03-10 12:02:52 4.8 STATUS STARTED qFDRP calculation Error in e$fun(obj, substitute(ex), parent.frame(), e$data) : worker initialization failed: there is no package called ‘RnBeads’
Just to check if you have any idea for this error?
Thanks! Rong
schmic05
commented
3 years ago Hi Rong,
It seems as if the installation of RnBeads has not been successful, can you try to re-install using:
source('https://rnbeads.org/data/install.R')
and then validate using
library(RnBeads)
Best, Michael
I installed WSH R package in R 4.0.3
When I run the test example, I am seeing:
R
This is the session info:
Matrix products: default BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.3.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] grid stats4 parallel stats graphics grDevices utils
[8] datasets methods base
other attached packages: [1] WSH_0.1.5
[2] RnBeads.hg38_1.22.0
[3] RUnit_0.4.32
[4] doParallel_1.0.16
[5] rtracklayer_1.50.0
[6] GenomicAlignments_1.26.0
[7] Rsamtools_2.6.0
[8] RnBeads_2.8.0
[9] plyr_1.8.6
[10] methylumi_2.36.0
[11] minfi_1.36.0
[12] bumphunter_1.32.0
[13] locfit_1.5-9.4
[14] iterators_1.0.13
[15] foreach_1.5.1
[16] Biostrings_2.58.0
[17] XVector_0.30.0
[18] SummarizedExperiment_1.20.0
[19] MatrixGenerics_1.2.1
[20] FDb.InfiniumMethylation.hg19_2.2.0
[21] org.Hs.eg.db_3.12.0
[22] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 [23] GenomicFeatures_1.42.1
[24] AnnotationDbi_1.52.0
[25] reshape2_1.4.4
[26] scales_1.1.1
[27] Biobase_2.50.0
[28] illuminaio_0.32.0
[29] matrixStats_0.58.0
[30] limma_3.46.0
[31] gridExtra_2.3
[32] gplots_3.1.1
[33] ggplot2_3.3.3
[34] fields_11.6
[35] spam_2.6-0
[36] dotCall64_1.0-1
[37] ff_4.0.4
[38] bit_4.0.4
[39] cluster_2.1.0
[40] MASS_7.3-53
[41] GenomicRanges_1.42.0
[42] GenomeInfoDb_1.26.2
[43] IRanges_2.24.1
[44] S4Vectors_0.28.1
[45] BiocGenerics_0.36.0
loaded via a namespace (and not attached): [1] colorspace_2.0-0 ellipsis_0.3.1
[3] siggenes_1.64.0 mclust_5.4.7
[5] base64_2.0 rstudioapi_0.13
[7] bit64_4.0.5 xml2_1.3.2
[9] splines_4.0.3 codetools_0.2-16
[11] sparseMatrixStats_1.2.1 scrime_1.3.5
[13] cachem_1.0.4 annotate_1.68.0
[15] dbplyr_2.1.0 HDF5Array_1.18.1
[17] readr_1.4.0 compiler_4.0.3
[19] httr_1.4.2 assertthat_0.2.1
[21] Matrix_1.2-18 fastmap_1.1.0
[23] prettyunits_1.1.1 tools_4.0.3
[25] gtable_0.3.0 glue_1.4.2
[27] GenomeInfoDbData_1.2.4 dplyr_1.0.4
[29] maps_3.3.0 rappdirs_0.3.3
[31] doRNG_1.8.2 Rcpp_1.0.6
[33] vctrs_0.3.6 rhdf5filters_1.2.0
[35] multtest_2.46.0 nlme_3.1-149
[37] preprocessCore_1.52.1 DelayedMatrixStats_1.12.3 [39] stringr_1.4.0 lifecycle_1.0.0
[41] rngtools_1.5 gtools_3.8.2
[43] XML_3.99-0.5 beanplot_1.2
[45] zlibbioc_1.36.0 hms_1.0.0
[47] GEOquery_2.58.0 rhdf5_2.34.0
[49] RColorBrewer_1.1-2 curl_4.3
[51] memoise_2.0.0 biomaRt_2.46.3
[53] reshape_0.8.8 stringi_1.5.3
[55] RSQLite_2.2.3 genefilter_1.72.1
[57] caTools_1.18.1 BiocParallel_1.24.1
[59] rlang_0.4.10 pkgconfig_2.0.3
[61] bitops_1.0-6 nor1mix_1.3-0
[63] lattice_0.20-41 purrr_0.3.4
[65] Rhdf5lib_1.12.1 tidyselect_1.1.0
[67] magrittr_2.0.1 R6_2.5.0
[69] generics_0.1.0 DelayedArray_0.16.1
[71] DBI_1.1.1 pillar_1.4.7
[73] withr_2.4.1 survival_3.2-7
[75] RCurl_1.98-1.2 tibble_3.0.6
[77] crayon_1.4.1 KernSmooth_2.23-17
[79] BiocFileCache_1.14.0 progress_1.2.2
[81] data.table_1.13.6 blob_1.2.1
[83] digest_0.6.27 xtable_1.8-4
[85] tidyr_1.1.2 openssl_1.4.3
[87] munsell_0.5.0 quadprog_1.5-8
[89] askpass_1.1