Error installing MBatch in R (WIndows 10)

[gabbyteku]

Hi,
I tried installing MBatch in R following the installation instructions. Th instalation failled after executing devtools::install_github("MD-Anderson-Bioinformatics/MBatch/package").
The error message was as follows:

Error: Failed to install 'MBatch' from GitHub:
lazy-load database 'C:/Users/gtu/Documents/R/R-3.6.1/library/prettyunits/R/prettyunits.rdb' is corrupt
In addition: Warning messages:
1: In paste0(" (", pretty_dt(elapsed), ")") :
restarting interrupted promise evaluation
2: In paste0(" (", pretty_dt(elapsed), ")") :
internal error -3 in R_decompress1

The system and R information is as follows:

sysname release version machine
"Windows" "10 x64" "build 18362" "x86-64"

getRversion()
[1] ‘3.6.1’

[TDCasasent]

Given the path "R/R-3.6.1/library/prettyunits/R/prettyunits.rdb" and the message that prettyunits "is corrupt", that sounds like a local problem with your installation of R. I would try uninstalling and re-installing prettyunits and/or your full R installation.

[gabbyteku]

Hi Casasent,
I just uninstalled prettyunits, reinstalled a new copy, then retried installing MBatch (I tried twice).
The error has changed to the following:

Error: Failed to install 'MBatch' from GitHub:
(converted from warning) installation of package ‘C:/Users/.../MBatch_1.4.17.tar.gz’ had non-zero exit status

[TDCasasent]

I just noticed this was in the older MBatch release. Can you try the new one at https://github.com/MD-Anderson-Bioinformatics/BatchEffectsPackage

The install process is the same, except a different path for the GitHub repo install.

If you get this same error, there will be more warnings or errors in the logs somewhere. Can you please find and post them, or the complete install log?

You can also choose to use the available Docker container instead, which is described in the newer package release given above.

[gabbyteku]

I can't seem to install the package with the above url.
devtools can't find the url and reports a 404 error.

Error: Failed to install 'unknown package' from GitHub:
HTTP error 404.
Not Found
Did you spell the repo owner (MD-Anderson-Bioinformatics) and repo name (MBatchPackage) correctly?

• If spelling is correct, check that you have the required permissions to access the repo.

[TDCasasent]

Helping will be easier if you specifically show me what you typed/ran. From above, I cannot tell what you ran.

I think the problem was the string in the devtools::install_github call. Check the updated page, which should show devtools::install_github("MD-Anderson-Bioinformatics/BatchEffectsPackage/apps/MBatch")

[gabbyteku]

I copied and pasted the uri above, that is,

devtool-cmd

I got the following message:

Error message:

Error: Failed to install 'MBatch' from GitHub:
(converted from warning) installation of package ‘C:/Users/gtu/AppData/Local/Temp/RtmpuSWqT1/file4fac6ea573af/MBatch_1.5.2.tar.gz’ had non-zero exit status

[TDCasasent]

There should be more logging with additional text. Can you please post the entire log, including your call to install_github? See the attached file for an example--the install works fine here, which strongly indicates an issue with your platform.

Chances are you do not have a prerequisite installed or rJava is mis-configured.

test.log