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yezhengSTAT / ADTnorm

ADTnorm normalizes the cell surface protein measurement of CITE-seq data, facilitating across batches and across studies data integration.
https://yezhengstat.github.io/ADTnorm/articles/ADTnorm-tutorial.html
GNU General Public License v3.0
20 stars 4 forks source link

Unable to download ADTnomr #15

Open adelpinoherrera opened 4 months ago

adelpinoherrera commented 4 months ago

Hello,

I have been trying to download ADTnorm and use it and I keep running into this error: ERROR: dependency ?flowStats? is not available for package ?ADTnorm? I have followed the instructions of remotes::install_github("yezhengSTAT/ADTnorm", build_vignettes = FALSE, lib=libraryPath) and also I have tried to install the flowWorKspace and flowCore individually and that didn't fix the issue. This is my session info:

R version 4.1.2 (2021-11-01) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.6 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C 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

other attached packages: [1] remotes_2.5.0

loaded via a namespace (and not attached): [1] ps_1.7.6 prettyunits_1.2.0 crayon_1.5.2 withr_3.0.0 rprojroot_2.0.4 R6_2.5.1 rlang_1.1.3
[8] cli_3.6.2 curl_5.2.0 rstudioapi_0.15.0 callr_3.7.3 tools_4.1.2 compiler_4.1.2 processx_3.8.3
[15] pkgbuild_1.3.1 sessioninfo_1.2.2 tcltk_4.1.2

yezhengSTAT commented 4 months ago

Quick answer is that the "flowStats" R package is needed, which theoretically should be installed automatically. Let me look into it.

yezhengSTAT commented 4 months ago

Not sure if you allowed the update of the package during the installation. I just tried it on a new environment and it is installed successfully.

adelpinoherrera commented 4 months ago

I would be more than happy to install the update. Could you send me the steps to do so please? And what version of R should I be using to make sure everything runs smoothly?

yezhengSTAT commented 4 months ago

Whops, I mean when you put in remotes::install_github("yezhengSTAT/ADTnorm", build_vignettes = FALSE), R may ask you whether you want to update a few packages that includes the dependency packages that need to be installed (type in 1 to update all). I think R 4.1 should be fine. On my side, I used R 4.3.

R version 4.3.2 (2023-10-31) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(ADTnorm)
Error in library(ADTnorm) : there is no package called ‘ADTnorm’
> remotes::install_github("yezhengSTAT/ADTnorm", build_vignettes = FALSE)
Downloading GitHub repo yezhengSTAT/ADTnorm@HEAD
── R CMD build ──────────────────────────────────────────────────────────────────────
✔  checking for file ‘/private/var/folders/1q/34zkg7xj5_q0sylw1_bccdzc0000gq/T/RtmpCRAeGd/remotesa1f677319969/yezhengSTAT-ADTnorm-fd5911b/DESCRIPTION’ ...
─  preparing ‘ADTnorm’:
✔  checking DESCRIPTION meta-information
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘ADTnorm_1.0.tar.gz’

* installing *source* package ‘ADTnorm’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ADTnorm)
adelpinoherrera commented 4 months ago

Hello Ye Zheng,

Thank you so much for your help. I ran what you suggested and i got this error ERROR: dependencies 'flowCore', 'flowWorkspace', 'ncdfFlow', 'flowViz' are not available for package 'flowStats'

All the best,

Adriana Del Pino Herrera (she/they)

PhD Student | Biomedical Engineering

BEAT Cancer Lab | University of Florida

Vice-president, BME GSC

President, BME Inclusive Excellence

J Crayton Pruitt Family Department of Biomedical Engineering

Phone: 412-417-1815

[cid:a09a30a0-c85d-4fbf-a90f-c1eaf3c0d80c][cid:96d7821d-8867-4e0b-8d2a-5196e649c76d]

From: Ye Zheng @.> Sent: Thursday, June 13, 2024 8:05 PM To: yezhengSTAT/ADTnorm @.> Cc: Del Pino Herrera, Adriana @.>; Author @.> Subject: Re: [yezhengSTAT/ADTnorm] Unable to download ADTnomr (Issue #15)

[External Email]

Whops, I mean when you put in remotes::install_github("yezhengSTAT/ADTnorm", build_vignettes = FALSE), R may ask you whether you want to update a few packages that includes the dependency packages that need to be installed (type in 1 to update all). I think R 4.1 should be fine. On my side, I used R 4.3.

`R version 4.3.2 (2023-10-31) -- "Eye Holes" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.

library(ADTnorm) Error in library(ADTnorm) : there is no package called ‘ADTnorm’ remotes::install_github("yezhengSTAT/ADTnorm", build_vignettes = FALSE) Downloading GitHub repo @.*** ── R CMD build ────────────────────────────────────────────────────────────────────── ✔ checking for file ‘/private/var/folders/1q/34zkg7xj5_q0sylw1_bccdzc0000gq/T/RtmpCRAeGd/remotesa1f677319969/yezhengSTAT-ADTnorm-fd5911b/DESCRIPTION’ ... ─ preparing ‘ADTnorm’: ✔ checking DESCRIPTION meta-information ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ building ‘ADTnorm_1.0.tar.gz’

— Reply to this email directly, view it on GitHubhttps://github.com/yezhengSTAT/ADTnorm/issues/15#issuecomment-2166981475, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AWB7E5J2E2ZJXTY4CVLYFELZHIXT5AVCNFSM6AAAAABJJKHMZOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNRWHE4DCNBXGU. You are receiving this because you authored the thread.Message ID: @.***>

yezhengSTAT commented 4 months ago

That is weird. Those dependence package should be installed automatically as well......See below:

> remove.packages("flowStats")
Removing package from ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
(as ‘lib’ is unspecified)
> remove.packages("flowViz")
Removing package from ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
(as ‘lib’ is unspecified)
> remove.packages("flowWorkspace")
Removing package from ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
(as ‘lib’ is unspecified)
> remove.packages("ncdfFlow")
Removing package from ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
(as ‘lib’ is unspecified)
> remotes::install_github("yezhengSTAT/ADTnorm", build_vignettes = FALSE)
Downloading GitHub repo yezhengSTAT/ADTnorm@HEAD
Installing 5 packages: flowCore, ncdfFlow, flowViz, flowWorkspace, flowStats
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/bin/macosx/big-sur-arm64/contrib/4.3:
  cannot open URL 'https://bioconductor.org/packages/3.17/data/annotation/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/bin/macosx/big-sur-arm64/contrib/4.3:
  cannot open URL 'https://bioconductor.org/packages/3.17/data/experiment/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/workflows/bin/macosx/big-sur-arm64/contrib/4.3:
  cannot open URL 'https://bioconductor.org/packages/3.17/workflows/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES'
trying URL 'https://bioconductor.org/packages/3.17/bioc/bin/macosx/big-sur-arm64/contrib/4.3/flowCore_2.12.2.tgz'
Content type 'application/x-compressed-tar' length 8529869 bytes (8.1 MB)
==================================================
downloaded 8.1 MB

trying URL 'https://bioconductor.org/packages/3.17/bioc/bin/macosx/big-sur-arm64/contrib/4.3/ncdfFlow_2.46.0.tgz'
Content type 'application/x-compressed-tar' length 1923945 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://bioconductor.org/packages/3.17/bioc/bin/macosx/big-sur-arm64/contrib/4.3/flowViz_1.64.0.tgz'
Content type 'application/x-compressed-tar' length 1289737 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'https://bioconductor.org/packages/3.17/bioc/bin/macosx/big-sur-arm64/contrib/4.3/flowWorkspace_4.12.2.tgz'
Content type 'application/x-compressed-tar' length 4935653 bytes (4.7 MB)
==================================================
downloaded 4.7 MB

trying URL 'https://bioconductor.org/packages/3.17/bioc/bin/macosx/big-sur-arm64/contrib/4.3/flowStats_4.12.0.tgz'
Content type 'application/x-compressed-tar' length 12255061 bytes (11.7 MB)
==================================================
downloaded 11.7 MB

The downloaded binary packages are in
    /var/folders/1q/34zkg7xj5_q0sylw1_bccdzc0000gq/T//RtmpCRAeGd/downloaded_packages
── R CMD build ──────────────────────────────────────────────────────────────────────
✔  checking for file ‘/private/var/folders/1q/34zkg7xj5_q0sylw1_bccdzc0000gq/T/RtmpCRAeGd/remotesa1f618e7da27/yezhengSTAT-ADTnorm-2dfa6ba/DESCRIPTION’ ...
─  preparing ‘ADTnorm’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘ADTnorm_1.0.tar.gz’

* installing *source* package ‘ADTnorm’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ADTnorm)
> library(ADTnorm)

Maybe you can try remotes::install_github("yezhengSTAT/ADTnorm", build_vignettes = FALSE, dependencies = TRUE) or just install those missing packages manually.

adelpinoherrera commented 4 months ago

Hello,

Sorry for bothering you again. I keep encountering these errors when downloading the package ERROR: dependency ‘flowStats’ is not available for package ‘ADTnorm’

All the best,

Adriana Del Pino Herrera (she/they)

PhD Student | Biomedical Engineering

BEAT Cancer Lab | University of Florida

Vice-president, BME GSC

President, BME Inclusive Excellence

J Crayton Pruitt Family Department of Biomedical Engineering

Phone: 412-417-1815

[cid:ce977715-50df-4ce5-bae6-d0bf193e8d64][cid:68cd28fc-c548-41d6-8f28-6cc43722fc20]

From: Ye Zheng @.> Sent: Thursday, June 13, 2024 9:03 PM To: yezhengSTAT/ADTnorm @.> Cc: Del Pino Herrera, Adriana @.>; Author @.> Subject: Re: [yezhengSTAT/ADTnorm] Unable to download ADTnomr (Issue #15)

[External Email]

That is weird. Those dependence package should be installed automatically as well......See below:

remove.packages("flowStats") Removing package from ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ (as ‘lib’ is unspecified) remove.packages("flowViz") Removing package from ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ (as ‘lib’ is unspecified) remove.packages("flowWorkspace") Removing package from ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ (as ‘lib’ is unspecified) remove.packages("ncdfFlow") Removing package from ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ (as ‘lib’ is unspecified) remotes::install_github("yezhengSTAT/ADTnorm", build_vignettes = FALSE) Downloading GitHub repo @.*** Installing 5 packages: flowCore, ncdfFlow, flowViz, flowWorkspace, flowStats Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/bin/macosx/big-sur-arm64/contrib/4.3: cannot open URL 'https://bioconductor.org/packages/3.17/data/annotation/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/bin/macosx/big-sur-arm64/contrib/4.3: cannot open URL 'https://bioconductor.org/packages/3.17/data/experiment/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.17/workflows/bin/macosx/big-sur-arm64/contrib/4.3: cannot open URL 'https://bioconductor.org/packages/3.17/workflows/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES' trying URL 'https://bioconductor.org/packages/3.17/bioc/bin/macosx/big-sur-arm64/contrib/4.3/flowCore_2.12.2.tgz' Content type 'application/x-compressed-tar' length 8529869 bytes (8.1 MB)

downloaded 8.1 MB

trying URL 'https://bioconductor.org/packages/3.17/bioc/bin/macosx/big-sur-arm64/contrib/4.3/ncdfFlow_2.46.0.tgz' Content type 'application/x-compressed-tar' length 1923945 bytes (1.8 MB)

downloaded 1.8 MB

trying URL 'https://bioconductor.org/packages/3.17/bioc/bin/macosx/big-sur-arm64/contrib/4.3/flowViz_1.64.0.tgz' Content type 'application/x-compressed-tar' length 1289737 bytes (1.2 MB)

downloaded 1.2 MB

trying URL 'https://bioconductor.org/packages/3.17/bioc/bin/macosx/big-sur-arm64/contrib/4.3/flowWorkspace_4.12.2.tgz' Content type 'application/x-compressed-tar' length 4935653 bytes (4.7 MB)

downloaded 4.7 MB

trying URL 'https://bioconductor.org/packages/3.17/bioc/bin/macosx/big-sur-arm64/contrib/4.3/flowStats_4.12.0.tgz' Content type 'application/x-compressed-tar' length 12255061 bytes (11.7 MB)

downloaded 11.7 MB

The downloaded binary packages are in /var/folders/1q/34zkg7xj5_q0sylw1_bccdzc0000gq/T//RtmpCRAeGd/downloaded_packages ── R CMD build ────────────────────────────────────────────────────────────────────── ✔ checking for file ‘/private/var/folders/1q/34zkg7xj5_q0sylw1_bccdzc0000gq/T/RtmpCRAeGd/remotesa1f618e7da27/yezhengSTAT-ADTnorm-2dfa6ba/DESCRIPTION’ ... ─ preparing ‘ADTnorm’: ✔ checking DESCRIPTION meta-information ... ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ building ‘ADTnorm_1.0.tar.gz’

Maybe you can try remotes::install_github("yezhengSTAT/ADTnorm", build_vignettes = FALSE, dependencies = TRUE) or just install those missing packages manually.

— Reply to this email directly, view it on GitHubhttps://github.com/yezhengSTAT/ADTnorm/issues/15#issuecomment-2167028904, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AWB7E5MQNATNPLDITNIN3WTZHI6ODAVCNFSM6AAAAABJJKHMZOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNRXGAZDQOJQGQ. You are receiving this because you authored the thread.Message ID: @.***>

yezhengSTAT commented 4 months ago

Sorry to hear that. I guess you need to look into the previous error messages, which may tell you why cytolib, flowWorkspace and flowStats packages cannot be installed. You may also consider installing those failed packages manually or consult with your server administrator regarding the installation of those dependency packages.

Thanks, Ye

aathbt commented 2 months ago

Hello @adelpinoherrera

I just had the same problem. This is caused by some version incompabilities between dependencies.

Under R 4.4.1, it should be pretty easy to solve:

However, this is much more complicated for R 4.1.2 because it is quite old (almost 3 years now) and a lot of dependency requirements have changed. If you want to get ADTnorm working with this version, you need to find which packages are incompatible and preventing the installation of the flow* packages and install specific versions that are matching the requirements. This is not easy to do and will probably take a lot of time.

I would recommend to update your R version to at least 4.3.*. If you need to keep R 4.1.2, you can always create a dedicated environment (for example with conda or a container) with a recent version of R and install ADTnorm in it.

yezhengSTAT commented 2 months ago

Thank you, Antonin, for sharing! Indeed, using R 4.3 or newer should solve many unwanted issues.

Thanks, Ye