Error while installing microbiomeSeq

[Gian77]

Hello, I wanted to try microbiomeSeq, but I ended up with the following namesapceExport error during installation:

Error: package or namespace load failed for ‘microbiomeSeq’ in namespaceExport(ns, exports): undefined exports: differential_expression, kruskal_expression Error: loading failed Execution halted ERROR: loading failed

• removing ‘/home/gian/R/x86_64-pc-linux-gnu-library/3.4/microbiomeSeq’ Installation failed: Command failed (1)

This is my sessionInfo()

sessionInfo() R version 3.4.1 (2017-06-30) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.3 LTS

Matrix products: default BLAS: /usr/lib/libblas/libblas.so.3.6.0 LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale: [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
[5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8
[7] LC_PAPER=en_CA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] BiocInstaller_1.26.1 devtools_1.13.3

loaded via a namespace (and not attached): [1] httr_1.3.1 compiler_3.4.1 R6_2.2.2 tools_3.4.1 withr_2.0.0
[6] curl_2.8.1 memoise_1.1.0 git2r_0.19.0 digest_0.6.12 tcltk_3.4.1

Thank you, Gian

[susheelbhanu]

Agree with Gian77. I'm seeing the same issue. Is there a stable version we can download and install?

[umerijaz]

Dear both, we are currently trying to fix the installation errors. Please allow us a bit of time to test the package properly. Best Wishes, Umer

[AlfredUg]

Dear Gian and susheelbhanu, the stable version will be availed as pointed out by Umer. Please kindly bear with us. I would also want to point out an error reported on another platform. 1. Error: package or namespace load failed for microbiomeSeq in dyn.load(file, DLLpath = DLLpath, ...):maximal number of DLLs reached ... To fix this error, there is need to increase the maximum number of DLLs which can be done by editing the ".Renviron" in the home directory of the system, one may consider creating one if it does not exist. For example , adding these two lines in .Renviron increases the maximum number of DLLs to 1000. Variable name=R_MAX_NUM_DLLS Value=1000

[susheelbhanu]

Thanks Umer.

I’ll edit the .Renviron as suggested.

Best, Susheel

From: Alfred Ssekagiri [mailto:notifications@github.com] Sent: Monday, October 23, 2017 5:56 AM To: umerijaz/microbiomeSeq microbiomeSeq@noreply.github.com Cc: Busi, Susheel Bhanu (MU-Student) sb6f4@mail.missouri.edu; Comment comment@noreply.github.com Subject: Re: [umerijaz/microbiomeSeq] Error while installing microbiomeSeq (#1)

Dear Gian and susheelbhanu, the stable version will be availed as pointed out by Umer. Please kindly bear with us. I would also want to point out an error reported on another platform.

1. Error: package or namespace load failed for microbiomeSeq in dyn.load(file, DLLpath = DLLpath, ...):maximal number of DLLs reached ... To fix this error, there is need to increase the maximum number of DLLs which can be done by editing the ".Renviron" in the home directory the system, one may consider creating one if it does not exist. For example , adding these two lines in .Renviron increases the maximum number of DLLs to 1000. Variable name=R_MAX_NUM_DLL Value=1000

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/umerijaz/microbiomeSeq/issues/1#issuecomment-338622612, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AJhHDd8_9L2EIu5V_Dog3g8-kY1Dtumtks5svHDCgaJpZM4PbZkA.

[lplaisance]

Hello all, I am running into a similar problem than described above, but increasing the maximum number of DLLs by creating an .Renviron file in my home directory doesn't do the trick. Now, I am very new to Rstudio and it is very possible I didn't set up the file correctly. I went to RStudio/File/New File/Text File and paste the text above and saved it as .Renviron in the default working directory set in my preferences. But I still get the following message:

Error: package or namespace load failed for ‘microbiomeSeq’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/multtest/libs/multtest.so': `maximal number of DLLs reached... In addition: Warning message: replacing previous import ‘igraph::diversity’ by ‘phangorn::diversity’ when loading ‘microbiomeSeq’

I have tried restarting RStudio and the readRenviron(".Renviron") command. I am on MacOS. Any suggestion on what I should be doing differently to make this work?

Thank you,

Lilly

[AlfredUg]

Hello lpaisance,

I am hoping that your default working directory is the home directory. I suggest you use R_MAX_NUM_DLLS=150 (just this one line) instead of the above example. For microbiomeSeq in particular, this should be enough. The reason as to why the previous example did not work for you could be that your machine is restricted to maximum number of DLLs less than 1000. Please remember to restart Rstudio thereafter.

I hope that helps with the installation.

Alfred.

[rizbak]

Hi AlfredUg .

i have same problem with Gian77 .

unable to load shared object '/usr/lib64/R/modules//lapack.so': `maximal number of DLLs reached... Warning: Error in chol2inv: LAPACK routines cannot be loaded

sessionInfo() R version 3.4.3 (2017-11-30) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS/LAPACK: /usr/lib64/R/lib/libRblas.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] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached): [1] compiler_3.4.3

i will to edit Variable name=R_MAX_NUM_DLLS in ".Renviron" but I did not find directory of ".Renviron". im used Centos 7. Thanks..

[AlfredUg]

@rizbak, I suggest you create the ".Renviron" file because it seems the system does not have one ; To achieve that, open the terminal (this should open in your home directory, if not, then navigate to your home directory) and do the following;

• type nano .Renviron
• In the screen that appears, type R_MAX_NUM_DLLS=150
• Press Ctrl + O followed by return
• Press Ctrl + X followed by return
• Close terminal and Rstudio (if you are using it).
• Restart Rstudio and install the package.

I hope that helps,

Thanks.

[rizbak]

Thanks for your suggest. My apps was worked..

Pada tanggal Jum, 2 Feb 2018 23.48, Alfred Ssekagiri < notifications@github.com> menulis:

@rizbak https://github.com/rizbak, I suggest you create the ".Renviron" file because it seems the system does not have one ; To achieve that, open the terminal (this should open in your home directory, if not, then navigate to your home directory) and do the following;

• type nano .Renviron
• In the screen that appears, type R_MAX_NUM_DLLS=150
• Press Ctrl + O followed by return
• Press Ctrl + X followed by return
• Close terminal and Rstudio (if you are using it).
• Restart Rstudio and install the package.

I hope that helps,

Thanks.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/umerijaz/microbiomeSeq/issues/1#issuecomment-362604090, or mute the thread https://github.com/notifications/unsubscribe-auth/AiUstTOhPUqhdscM4DiiDjkj3qrMGR2nks5tQx5RgaJpZM4PbZkA .

[siobhon-egan]

Just wondering if this has been solved? I am running into the same issue.

RStudio output

install_github("umerijaz/microbiomeSeq")
Downloading GitHub repo umerijaz/microbiomeSeq@master
from URL https://api.github.com/repos/umerijaz/microbiomeSeq/zipball/master
Installing microbiomeSeq
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL  \
  '/private/var/folders/c1/1wk2dj0s543fp9k7jh695ndw0000gn/T/Rtmp0S2TJ6/devtools6df368361daa/umerijaz-microbiomeSeq-ce63464'  \
  --library='/Library/Frameworks/R.framework/Versions/3.5/Resources/library' --install-tests 

ERROR: dependency ‘DESeq2’ is not available for package ‘microbiomeSeq’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/microbiomeSeq’
Installation failed: Command failed (1)

[AlfredUg]

Heya @siobhon-egan

Your issue is due to a missing dependancy "DESeq2", ERROR: dependency ‘DESeq2’ is not available for package ‘microbiomeSeq’ . Please just make sure you have all the dependancies available, see full list here.

I hope that helps.

Alfred.

[nhungdoan1905]

hi, I was try to install microbiomeSeq packages, and what problems I got:

Installing 15 packages: DESeq2, KMDA, WGCNA, fso, randomForest, genefilter, locfit, geneplotter, RcppArmadillo, fastcluster, GO.db, labdsv, annotate, XML, Rtsne Error: Failed to install 'microbiomeSeq' from GitHub: (converted from warning) unable to access index for repository https://www.stats.ox.ac.uk/pub/RWin/bin/macosx/el-capitan/contrib/3.5: cannot open URL 'https://www.stats.ox.ac.uk/pub/RWin/bin/macosx/el-capitan/contrib/3.5/PACKAGES'

install.packages('microbiomeSeq', dependencies=TRUE, repos='http://cran.rstudio.com/') Warning in install.packages : package ‘microbiomeSeq’ is not available (for R version 3.5.0) how can I fix this