installation fails with "Skipping 1 packages not available: bamUtils"

[funnell]

Probably just missing bamUtils in your remotes

[mjko1210]

Hi, is there any update on this? I couldn't install the package with same issues.

** 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’.`

[imielinski]

Sorry for the late reply – we should update the install instructions.

You have to set this environment variable otherwise install_github errors out on any warning during package install (also for dependencies).

allows dependencies that throw warnings to install

Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS = TRUE)

May be good to put this in your .Rprofile or set the env variable in your .bash_profile

Marcin

From: mjko1210 notifications@github.com Reply-To: mskilab/JaBbA reply@reply.github.com Date: Tuesday, June 23, 2020 at 2:28 PM To: mskilab/JaBbA JaBbA@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: Re: [mskilab/JaBbA] installation fails with "Skipping 1 packages not available: bamUtils" (#24)

Hi, is there any update on this? I couldn't install the package with same issues.

** 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’.`

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https:/github.com/mskilab/JaBbA/issues/24*issuecomment-648338146__;Iw!!C6sPl7C9qQ!Ec5uknEfNxIxyuNHD9oYJoqTMayt0BQP7umA_bThTzYmotMimD4qPzlSQ8FSKLUcBzM$, or unsubscribehttps://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/ABFUFY44LRGMMXS2KBFSW5TRYDX3PANCNFSM4J6CWKLQ__;!!C6sPl7C9qQ!Ec5uknEfNxIxyuNHD9oYJoqTMayt0BQP7umA_bThTzYmotMimD4qPzlSQ8FS_yomDVo$.

---

This message is for the recipient’s use only, and may contain confidential, privileged or protected information. Any unauthorized use or dissemination of this communication is prohibited. If you received this message in error, please immediately notify the sender and destroy all copies of this message. The recipient should check this email and any attachments for the presence of viruses, as we accept no liability for any damage caused by any virus transmitted by this email.

[xtYao]

We removed bamUtils from the dependency chain. This is related to the Ppurple package which we also suspended in JaBbA until we reduce its dependency lists.