Problem installing microbiomSeq

[locon833]

Hi All,

I'm currently trying to download microbiomeSeq in RStudio and am getting the following error:

install_github("umerijaz/microbiomeSeq") Downloading GitHub repo umerijaz/microbiomeSeq@master Skipping 6 packages not available: AnnotationDbi, DESeq2, GO.db, impute, phyloseq, preprocessCore ✔ checking for file ‘/private/var/folders/kt/_6vrl2sd4r7dyqz24y1mn02c0000gn/T/RtmpMCGapV/remotesfc27a0784c/umerijaz-microbiomeSeq-ffa0090/DESCRIPTION’ ... ─ preparing ‘microbiomeSeq’: ✔ checking DESCRIPTION meta-information ... ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ looking to see if a ‘data/datalist’ file should be added ─ building ‘microbiomeSeq_0.1.tar.gz’

• installing source package ‘microbiomeSeq’ ... R data * moving datasets to lazyload DB byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ‘adespatial’ ERROR: lazy loading failed for package ‘microbiomeSeq’
• removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/microbiomeSeq’ Error in i.p(...) : (converted from warning) installation of package ‘/var/folders/kt/_6vrl2sd4r7dyqz24y1mn02c0000gn/T//RtmpMCGapV/filefc24bf0545d/microbiomeSeq_0.1.tar.gz’ had non-zero exit status

I tried running the command suggested in a previous thread without any luck:

defaults write org.R-project.R force.LANG en_US.UTF-8 Error: unexpected symbol in "defaults write"

Any thoughts on how to get this installed?

[AlfredUg]

Heya there, kindly make sure you have the dependencies installed and re-install microbiomeSeq. Check the previous thread to see how you can do this in a single step.

Thanks

On Monday, June 3, 2019, locon833 notifications@github.com wrote:

Hi All,

I'm currently trying to download microbiomeSeq in RStudio and am getting the following error:

installgithub("umerijaz/microbiomeSeq") Downloading GitHub repo umerijaz/microbiomeSeq@master Skipping 6 packages not available: AnnotationDbi, DESeq2, GO.db, impute, phyloseq, preprocessCore ✔ checking for file ‘/private/var/folders/kt/ 6vrl2sd4r7dyqz24y1mn02c0000gn/T/RtmpMCGapV/remotesfc27a0784c/umerijaz- microbiomeSeq-ffa0090/DESCRIPTION’ ... ─ preparing ‘microbiomeSeq’: ✔ checking DESCRIPTION meta-information ... ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ looking to see if a ‘data/datalist’ file should be added ─ building ‘microbiomeSeq_0.1.tar.gz’

• installing source package ‘microbiomeSeq’ ... R data * moving datasets to lazyload DB byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ‘adespatial’ ERROR: lazy loading failed for package ‘microbiomeSeq’
• removing ‘/Library/Frameworks/R.framework/Versions/3.5/ Resources/library/microbiomeSeq’ Error in i.p(...) : (converted from warning) installation of package ‘/var/folders/kt/_ 6vrl2sd4r7dyqz24y1mn02c0000gn/T//RtmpMCGapV/filefc24bf0545d/microbiomeSeq_0.1.tar.gz’ had non-zero exit status

I tried running the command suggested in a previous thread without any luck:

defaults write org.R-project.R force.LANG en_US.UTF-8 Error: unexpected symbol in "defaults write"

Any thoughts on how to get this installed?

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[heuklang]

I had the same problem. So I reinstalled "adespatial" and solved it.

---- R consol example ----

install.packages("adespatial") library(devtools) install_github("umerijaz/microbiomeSeq")

I hope you can solve the problem. Thanks.

[PabloArrow]

Install "adespatial" and then reinstall

[DhebbieF]

Hi please help... I have the same exact problem as stated in this thread, but in my case, all solutions I used have not solved my problem. The same error message is as follows:

install_github("umerijaz/microbiomeSeq") Downloading GitHub repo umerijaz/microbiomeSeq@HEAD Skipping 6 packages not available: AnnotationDbi, GO.db, preprocessCore, impute, phyloseq, DESeq2 ✓ checking for file ‘/private/var/folders/r0/dns1jnpd71578fvdq2shf14m0000gn/T/RtmpFPZs61/remotes37742b888ab/umerijaz-microbiomeSeq-ffa0090/DESCRIPTION’ ... ─ preparing ‘microbiomeSeq’: ✓ checking DESCRIPTION meta-information ... ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ building ‘microbiomeSeq_0.1.tar.gz’

• installing source package ‘microbiomeSeq’ ... using staged installation R ** data * moving datasets to lazyload DB byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ‘rncl’ Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted ERROR: lazy loading failed for package ‘microbiomeSeq’
• removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/microbiomeSeq’ Warning message: In i.p(...) : installation of package ‘/var/folders/r0/dns1jnpd71578fvdq2shf14m0000gn/T//RtmpFPZs61/file3776114b4c5/microbiomeSeq_0.1.tar.gz’ had non-zero exit status

(as seen in a previous thread to ensure all dependencies are installed) I independently installed all 6 dependencies it stated ( AnnotationDbi, GO.db, preprocessCore, impute, phyloseq, DESeq2) , using the following: BiocManager::install("DESeq2", force = TRUE) BiocManager::install("impute", force = TRUE) BiocManager::install("preprocessCore",force = TRUE) BiocManager::install("GO.db", force = TRUE) BiocManager::install("phyloseq", force = TRUE) BiocManager::install("AnnotationDbi", force = TRUE) BiocManager::install("adespatial", force = TRUE)

I used "force = TRUE" because it kept throwing a warning message as follows:

'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details replacement repositories: CRAN: https://cran.rstudio.com/ Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.1 (2021-08-10) Warning message: package(s) not installed when version(s) same as current; use force = TRUE to re-install: 'adespatial' (This was the same for all 6 of them)

But before this I got to this stage I had used BiocManager::install("DeSeq2")

and it gave a warning that

Package ‘GenomeInfoDb’ version 1.28.1 cannot be unloaded: Error in unloadNamespace(package) : namespace ‘GenomeInfoDb’ is imported by ‘Biostrings’ so cannot be unloaded In addition: Warning message: package ‘GenomeInfoDb’ was built under R version 4.1.1

Having read this, I upgraded my R version from R .4.1.0 to R. 4.1.1 and Im back to the very same error.

Please assist.. Thankyou.

My session info is as follows:

R version 4.1.1 (2021-08-10) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS High Sierra 10.13.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods
[9] base

other attached packages: [1] devtools_2.4.2 usethis_2.0.1 DESeq2_1.32.0
[4] SummarizedExperiment_1.22.0 Biobase_2.52.0 MatrixGenerics_1.4.3
[7] matrixStats_0.60.1 GenomicRanges_1.44.0 GenomeInfoDbData_1.2.6
[10] GenomeInfoDb_1.28.2 IRanges_2.26.0 S4Vectors_0.30.0
[13] BiocGenerics_0.38.0 phyloseq_1.36.0

loaded via a namespace (and not attached): [1] nlme_3.1-152 bitops_1.0-7 fs_1.5.0 bit64_4.0.5
[5] RColorBrewer_1.1-2 httr_1.4.2 rprojroot_2.0.2 tools_4.1.1
[9] utf8_1.2.2 R6_2.5.1 vegan_2.5-7 DBI_1.1.1
[13] mgcv_1.8-36 colorspace_2.0-2 permute_0.9-5 rhdf5filters_1.4.0
[17] ade4_1.7-17 withr_2.4.2 tidyselect_1.1.1 prettyunits_1.1.1
[21] processx_3.5.2 curl_4.3.2 bit_4.0.4 compiler_4.1.1
[25] microbiome_1.14.0 cli_3.0.1 desc_1.3.0 DelayedArray_0.18.0 [29] scales_1.1.1 genefilter_1.74.0 callr_3.7.0 stringr_1.4.0
[33] XVector_0.32.0 pkgconfig_2.0.3 sessioninfo_1.1.1 fastmap_1.1.0
[37] rlang_0.4.11 RSQLite_2.2.8 rstudioapi_0.13 generics_0.1.0
[41] jsonlite_1.7.2 BiocParallel_1.26.2 dplyr_1.0.7 RCurl_1.98-1.4
[45] magrittr_2.0.1 biomformat_1.20.0 Matrix_1.3-4 Rcpp_1.0.7
[49] munsell_0.5.0 Rhdf5lib_1.14.2 fansi_0.5.0 ape_5.5
[53] lifecycle_1.0.0 stringi_1.7.4 MASS_7.3-54 zlibbioc_1.38.0
[57] rhdf5_2.36.0 pkgbuild_1.2.0 Rtsne_0.15 plyr_1.8.6
[61] blob_1.2.2 grid_4.1.1 crayon_1.4.1 lattice_0.20-44
[65] Biostrings_2.60.2 splines_4.1.1 annotate_1.70.0 multtest_2.48.0
[69] KEGGREST_1.32.0 locfit_1.5-9.4 ps_1.6.0 pillar_1.6.2
[73] igraph_1.2.6 seqinr_4.2-8 geneplotter_1.70.0 reshape2_1.4.4
[77] codetools_0.2-18 pkgload_1.2.1 XML_3.99-0.7 glue_1.4.2
[81] mctoolsr_0.1.1.2 data.table_1.14.0 remotes_2.4.0 BiocManager_1.30.16 [85] png_0.1-7 vctrs_0.3.8 foreach_1.5.1 testthat_3.0.4
[89] gtable_0.3.0 purrr_0.3.4 tidyr_1.1.3 cachem_1.0.6
[93] ggplot2_3.3.5 xtable_1.8-4 survival_3.2-13 tibble_3.1.4
[97] iterators_1.0.13 AnnotationDbi_1.54.1 memoise_2.0.0 cluster_2.1.2
[101] ellipsis_0.3.2

Thank you.

[AlfredUg]

Hi @DhebbieF

Try the following to automatically get all the dependancies.

install.packages("adespatial")
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(c("AnnotationDbi", "DESeq2", "GO.db", "impute", "phyloseq", "preprocessCore"))

Then install microbiomeSeq via install_github("umerijaz/microbiomeSeq").

Alfred.