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mskilab-org / JaBbA

MIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data.
MIT License
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failed to install 'unknown package' from GitHub. #90

Open ryao-mdanderson opened 1 year ago

ryao-mdanderson commented 1 year ago

Dear KaBbA authors:

I tried install the package under module load R/4.2.1 by the command: devtools::install_github('mskilab/JaBbA')

Hit the similar message of ... The downloaded source packages are in ‘/tmp/Rtmp9JUgRy/downloaded_packages’ Error: Failed to install 'unknown package' from GitHub: Failed to install 'unknown package' from GitHub: Failed to install 'gChain' from GitHub: HTTP error 403. API rate limit exceeded for 143.111.84.242. (But here's the good news: Authenticated requests get a higher rate limit. Check out the documentation for more details.)

Rate limit remaining: 0/60 Rate limit reset at: 2023-06-19 23:04:12 UTC

To increase your GitHub API rate limit

I don't have a project with github.

May you please advise?

Regards, Rong

ryao-mdanderson commented 1 year ago

@pwaltman @imielinski @walaj @evanbiederstedt Dear JaBba authors: any suggestions for this reported issue? Thank you!

imielinski commented 1 year ago

Hi Rong - this is an issue with devtools::install_github that impacts some users and not others when dependencies get installed have you tried making a GITHUB_PAT token? should be a workaround while we investigate Marcin

ps also we recommend running jabba with R4.1 or earlier – there were some non back-compatible changes to base packages in R4.2 that we are trying to update our codebase for .. sorry for the inconvenience

-- Marcin Imieliński M.D., Ph.D. Lab head, www.mskilab.org https://github.com/mskilab

Interim Member of the Faculty Department of Pathology Director of Cancer Genetics Perlmutter Cancer Center NYU Grossman School of Medicine Assistant Attending Pathologist NYU Langone Health 550 1st Avenue, New York, NY em: @.*** ph: (617) 528-0211

Core Member New York Genome Center 101 6th Ave, New York, NY em: @.*** ph: (646) 977-7214

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ryao-mdanderson commented 1 year ago

@imielinski Hello Marcin,

Thank you for your suggestions. I do not have a github token, this is my first time to hit this problem. I think I will proceed with R/4.1 to see if it works there.

Regards, Rong

ryao-mdanderson commented 1 year ago

@imielinski Hello Marcin,

using R/4.1.0 hit the similar problem for github credential.

I research and find this article https://github.com/settings/tokens/new, however, i failed to open the page on HPC node to proceed.

Do you have an example how you proceed? Or any other work around?

Regards, Rong

shihabdider commented 1 year ago

If you wish to generate a personal access token (PAT), I suggest you take a look at this: https://stackoverflow.com/a/33668077/10302846

Alternatively, as a workaround, you can try cloning the JaBbA repo and loading the package locally:

# in your terminal
git clone "https://github.com/mskilab-org/JaBbA.git"

# in the R console or script
devtools::load_all('path/to/clone')
ryao-mdanderson commented 1 year ago

Thank you Shihab. @shihabdider

The workaround works for me.

Regards, Rong

shihabdider commented 11 months ago

26e9102099990c90304d75c051573609e55c4bf3 now installs Sequenza from the CRAN archive, which should fix this issue.

ryao-mdanderson commented 10 months ago

I revisit JaBbA installation for R/4.3.1 on RHEL8. @shihabdider : From the above comment Sequenza has been from CRAN archive, however,

devtools::install_github('mskilab/JaBbA') still hit : ERROR: dependency ‘sequenza’ is not available for package ‘JaBbA’

If I manually install sequenza:

install.packages("https://cran.r-project.org/src/contrib/Archive/sequenza/sequenza_3.0.0.tar.gz") hit the following message Installing package into ‘/rsrch3/home/itops/ryao/R/x86_64-pc-linux-gnu-library/4.3-jabba’ (as ‘lib’ is unspecified) inferring 'repos = NULL' from 'pkgs' trying URL 'https://cran.r-project.org/src/contrib/Archive/sequenza/sequenza_3.0.0.tar.gz' Content type 'application/x-gzip' length 3478653 bytes (3.3 MB)

downloaded 3.3 MB

ERROR: dependency ‘copynumber’ is not available for package ‘sequenza’

Then, if use BiocManager to install copynumber,

BiocManager::install("copynumber") Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.1 (2023-06-16) Installing package(s) 'BiocVersion', 'copynumber' trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/BiocVersion_3.18.0.tar.gz' Content type 'application/x-gzip' length 968 bytes

downloaded 968 bytes

The downloaded source packages are in ‘/tmp/Rtmp4IPVIR/downloaded_packages’ Installation paths not writeable, unable to update packages path: /risapps/rhel8/R/4.3.1/lib64/R/library packages: foreign, KernSmooth, lattice, Matrix, mgcv, nlme, rpart, spatial, survival Warning message: package ‘copynumber’ is not available for Bioconductor version '3.18'

The dependencies for JaBbA can't be installed. Do you have any suggestion? Thanks!

shihabdider commented 10 months ago

It looks like your Bioconductor version is not compatible with the version of copynumber you are attempting to install. In particular, it looks like Bioconductor 3.18 removed copynumber from its list of supported packages: https://www.bioconductor.org/about/removed-packages/

You may instead try the installation instructions given here: https://www.bioconductor.org/packages//2.12/bioc/html/copynumber.html

E.g

source("https://bioconductor.org/biocLite.R")
biocLite("copynumber")
ryao-mdanderson commented 10 months ago

Hello @shihabdider : Thank you for a reply with suggested approach. I tried the above method yesterday but the commands does not work as expected. I am reinstalling JaBbA on R/4.3.1 on RHEL8 from scratch, I will see if this time any luck.

Thank you, Rong

ryao-mdanderson commented 10 months ago

Hello JaBbA authors,

I use R/4.3.1 to install JaBbA on RHEL8, it does not work.

devtools::install_github('mskilab/JaBbA') hit error ERROR: dependency ‘sequenza’ is not available for package ‘JaBbA’

Tried

install.packages("https://cran.r-project.org/src/contrib/Archive/sequenza/sequenza_3.0.0.tar.gz") ERROR: dependency ‘copynumber’ is not available for package ‘sequenza’

Further to try

BiocManager::install("copynumber") package ‘copynumber’ is not available for Bioconductor version '3.18'

source("https://bioconductor.org/biocLite.R") Error: With R version 3.5 or greater, install Bioconductor packages using BiocManager; see https://bioconductor.org/install

Also tried:

install.packages("https://www.bioconductor.org/packages//2.12/bioc/src/contrib/copynumber_1.1.1.tar.gz") ... Error: object ‘DataFrame’ is not exported by 'namespace:IRanges'

NO luck to work on R/4.3.1.

shihabdider commented 10 months ago

I was able to reproduce your original issue with installing copynumber. It seems this package also needs to be installed via its source and a PR will be made/merged soon to implement this. In the meantime, here is some code which should fix the issue:

# Download and install copynumber from source
copynumber_url <- "https://www.bioconductor.org/packages/3.14/bioc/bin/macosx/contrib/4.1/copynumber_1.34.0.tgz"  
copynumber_path <- tempfile(fileext = ".tar.gz")
download.file(copynumber_url, copynumber_path, mode="wb")
install.packages(copynumber_path, repos = NULL, type = "source")

# Now download and install sequenza from source
package_url <- "https://cran.r-project.org/src/contrib/Archive/sequenza/sequenza_3.0.0.tar.gz"
package_path <- tempfile(fileext = ".tar.gz")
download.file(package_url, package_path, mode="wb")
install.packages(package_path, repos = NULL, type = "source")

# Check if installation was successful
library(sequenza)

# Now install JaBbA from github
devtools::install_github("mskilab-org/JaBbA", upgrade="never", force=TRUE)

Also for the original github token error (which may also be relevant to the above code), you will need to first generate a github PAT (go here) and then add this as an environment variable via export GITHUB_PAT="your-generated-token-here". You can append this to your .bashrc to avoid having to add it every time you open a new shell.

ryao-mdanderson commented 10 months ago

Hello @shihabdider Thank you for your reply. Follow your suggestion, I am able to install JaBaA under R/4.3.1.

Now I guess my goal is to have a test case working under R/4.1.0 or R/4.3.1, which is reported in issue #97.

Thanks again for your consistent support. Rong Yao