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lea
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@lea
Last seen 3.8 years ago
Hello,
I'm trying to install the ENmix package, I used BiocManager::install("ENmix") and it succesfully unpacked. But when I load it with library it says:
Erreur : package or namespace load failed for ‘ENmix’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
no package called ‘rtracklayer’ was found
Also : There were 13 warnings (use warnings() to see them)
I tried loading the package rtracklayer (BiocManager::install("rtracklayer")) and I had the error:
The downloaded source packages are in
‘C:\Users\User\AppData\Local\Temp\Rtmp8Uku7c\downloaded_packages’
Warning message:
In install.packages(...) :
installation of package ‘rtracklayer’ had non-zero exit status
I tried looking on the internet but I'm a beginner so I don't really get what I should do and some solution where on Linux so I can't try it. Thank you for your help!
sessionInfo( )
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=French_France.1252
[2] LC_CTYPE=French_France.1252
[3] LC_MONETARY=French_France.1252
[4] LC_NUMERIC=C
[5] LC_TIME=French_France.1252
attached base packages:
[1] stats4 parallel stats graphics grDevices
[6] utils datasets methods base
other attached packages:
[1] BiocInstaller_1.12.1
[2] SummarizedExperiment_1.20.0
[3] Biobase_2.50.0
[4] GenomicRanges_1.42.0
[5] GenomeInfoDb_1.26.2
[6] IRanges_2.24.1
[7] S4Vectors_0.28.1
[8] BiocGenerics_0.36.0
[9] MatrixGenerics_1.2.1
[10] matrixStats_0.58.0
[11] doParallel_1.0.16
[12] iterators_1.0.13
[13] foreach_1.5.1
loaded via a namespace (and not attached):
[1] bitops_1.0-6
[2] bit64_4.0.5
[3] RColorBrewer_1.1-2
[4] progress_1.2.2
[5] httr_1.4.2
[6] dynamicTreeCut_1.63-1
[7] tools_4.0.2
[8] doRNG_1.8.2
[9] nor1mix_1.3-0
[10] utf8_1.1.4
[11] R6_2.5.0
[12] HDF5Array_1.18.1
[13] DBI_1.1.1
[14] rhdf5filters_1.2.0
[15] tidyselect_1.1.0
[16] prettyunits_1.1.1
[17] base64_2.0
[18] curl_4.3
[19] bit_4.0.4
[20] compiler_4.0.2
[21] preprocessCore_1.52.1
[22] xml2_1.3.2
[23] DelayedArray_0.16.2
[24] RPMM_1.25
[25] genefilter_1.72.1
[26] askpass_1.1
[27] rappdirs_0.3.3
[28] stringr_1.4.0
[29] digest_0.6.27
[30] illuminaio_0.32.0
[31] siggenes_1.64.0
[32] XVector_0.30.0
[33] pkgconfig_2.0.3
[34] scrime_1.3.5
[35] sparseMatrixStats_1.2.1
[36] dbplyr_2.1.0
[37] fastmap_1.1.0
[38] limma_3.46.0
[39] rlang_0.4.10
[40] rstudioapi_0.13
[41] RSQLite_2.2.3
[42] impute_1.64.0
[43] DelayedMatrixStats_1.12.3
[44] generics_0.1.0
[45] mclust_5.4.7
[46] BiocParallel_1.24.1
[47] dplyr_1.0.4
[48] RCurl_1.98-1.2
[49] magrittr_2.0.1
[50] GenomeInfoDbData_1.2.4
[51] Matrix_1.3-2
[52] fansi_0.4.2
[53] Rcpp_1.0.6
[54] Rhdf5lib_1.12.1
[55] lifecycle_1.0.0
[56] stringi_1.5.3
[57] MASS_7.3-53.1
[58] zlibbioc_1.36.0
[59] BiocFileCache_1.14.0
[60] rhdf5_2.34.0
[61] plyr_1.8.6
[62] grid_4.0.2
[63] blob_1.2.1
[64] crayon_1.4.1
[65] lattice_0.20-41
[66] Biostrings_2.58.0
[67] splines_4.0.2
[68] multtest_2.46.0
[69] annotate_1.68.0
[70] hms_1.0.0
[71] locfit_1.5-9.4
[72] pillar_1.5.0
[73] beanplot_1.2
[74] rngtools_1.5
[75] geneplotter_1.68.0
[76] codetools_0.2-18
[77] biomaRt_2.46.3
[78] glue_1.4.2
[79] XML_3.99-0.5
[80] BiocManager_1.30.10
[81] vctrs_0.3.6
[82] purrr_0.3.4
[83] openssl_1.4.3
[84] assertthat_0.2.1
[85] reshape_0.8.8
[86] cachem_1.0.4
[87] xfun_0.21
[88] xtable_1.8-4
[89] survival_3.2-7
[90] tibble_3.1.0
[91] tinytex_0.29
[92] AnnotationDbi_1.52.0
[93] memoise_2.0.0
[94] cluster_2.1.1
[95] ellipsis_0.3.1
Hello, thank for your answer!
You're right I forgot the error message, it says:
I tried to check the validity of the BiocManager package and it says "True" so I guess at leats everything is fine on this part.
Does installing zlibbioc help? I can install the source version on Windows, and it makes repeated calls to zlibbioc.
No but I'm not sure it even install zlibbioc when I asked since I had this response with a "permission denied" at the end:
Ah, that explains it. When R installs a package, it first creates a directory in your library dir called 00LOCK and does a preliminary install there. You can see that from your install of isoband:
And at the very end of your output you can see that there is already a 00LOCK-zlibbioc directory, which means that a previous install probably had problems and only got half installed. So you need to either do
Which should remove that dir, and then you can try installing zlibbioc again. You might also try
as well, to ensure it's fully removed.
Ugh. You need to convert the back slashes in the call to
unlinkto forward slashes or R will get all huffy with you.I tried both (with the slashes the other way around), it did not work but I delete the package directly on my file browser and it correctly downloads the zlibbioc package. Unfortunately, I tried installing the package rtracklayer again after and it did not change anything.
Will you give the full output that you get when installing?
Yes, it is quite long so I had to divide it.
OK. That's super weird. What do you get from
I get the same thing as you
I put the output that I got when installing rtracklayer, not zlibbiocif if that was what you were asking.