installation error: "Error: package or namespace load failed for ‘bamUtils’"

[funnell]

Error loading bamUtils. However, just running library(bamUtils) completed. I installed bamUtils using devtools right before attempting to install Ppurple.

─  preparing ‘Ppurple’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘Ppurple_0.2.0.tar.gz’

Installing package into ‘/home/tyler/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
* installing *source* package ‘Ppurple’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for ‘bamUtils’:
 (converted from warning) replacing previous import ‘GenomicRanges::shift’ by ‘data.table::shift’ when loading ‘bamUtils’
Error: package ‘bamUtils’ could not be loaded
Execution halted
ERROR: lazy loading failed for package ‘Ppurple’
* removing ‘/home/tyler/R/x86_64-pc-linux-gnu-library/3.6/Ppurple’```

[mskilab]

Thanks! Will look into this ..

On Fri, Dec 20, 2019 at 4:19 PM Tyler Funnell notifications@github.com wrote:

Error loading bamUtils. However, just running library(bamUtils) completed. I installed bamUtils using devtools right before attempting to install Ppurple.

─ preparing ‘Ppurple’:

✔ checking DESCRIPTION meta-information ...

─ checking for LF line-endings in source and make files and shell scripts

─ checking for empty or unneeded directories

─ building ‘Ppurple_0.2.0.tar.gz’

Installing package into ‘/home/tyler/R/x86_64-pc-linux-gnu-library/3.6’

(as ‘lib’ is unspecified)

• installing source package ‘Ppurple’ ...

** using staged installation

** R

** inst

** byte-compile and prepare package for lazy loading

Error: package or namespace load failed for ‘bamUtils’:

(converted from warning) replacing previous import ‘GenomicRanges::shift’ by ‘data.table::shift’ when loading ‘bamUtils’

Error: package ‘bamUtils’ could not be loaded

Execution halted

ERROR: lazy loading failed for package ‘Ppurple’

• removing ‘/home/tyler/R/x86_64-pc-linux-gnu-library/3.6/Ppurple’```

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[mjko1210]

Hi, Is there any update on this? I got the same error when I was installing JaBbA devtools::install_github('mskilab/JaBbA')

[imielinski]

Right same issue – we will update the install instructions. Thanks for pointing out

Set this in your .Rprofile or set the env variable in your .bash_profile

allows dependencies that throw warnings to install

Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS = TRUE)

From: mjko1210 notifications@github.com Reply-To: mskilab/Ppurple reply@reply.github.com Date: Tuesday, June 23, 2020 at 2:08 PM To: mskilab/Ppurple Ppurple@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: Re: [mskilab/Ppurple] installation error: "Error: package or namespace load failed for ‘bamUtils’" (#1)

Hi, Is there any update on this? I got the same error when I was installing JaBbA devtools::install_github('mskilab/JaBbA')

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