Annotation issue and Rscript error

[nick-webster]

Hi, I was trying to use an annotation file that was originally generated in ESPRESSO as it contains novel isoforms that are not present in the supplied files. ESPRESSO created an updated .gtf that I converted to .GFF3 using AGAT. When I run TappAS I get the following error:

logMsg exception: /tappas.log (Read-only file system)15:32 - Checking specified annotation file: /Users/nickwebster/updated.gff3
logMsg exception: /tappas.log (Read-only file system)15:32 - Checking design file: /Users/nickwebster/anaconda3/envs/rmats-long/design_file.txt
logMsg exception: /tappas.log (Read-only file system)15:32 - Design file passed initial check.
logMsg exception: /tappas.log (Read-only file system)15:32 - Checking specified matrix file (Two_Group_Comparison): /Users/nickwebster/anaconda3/envs/rmats-long/sample_matrix.txt
logMsg exception: /tappas.log (Read-only file system)15:32 - Matrix file passed initial check.
logMsg exception: /tappas.log (Read-only file system)15:32 - The custom annotation file has been modified. We are going to load the version you used to create the project.
logMsg exception: /tappas.log (Read-only file system)15:32 - Annotation loaded correctly. Check if the project contains the correct annotation or you want to create a new one.
logMsg exception: /tappas.log (Read-only file system)15:32 - Input Data dialog results: tappas.DlgInputData$Params@5de8c8db
logMsg exception: /tappas.log (Read-only file system)15:32 - The custom annotation file has been modified. We are going to load the version you used to create the project.
logMsg exception: /tappas.log (Read-only file system)15:32 - Annotation loaded correctly. Check if the project contains the correct annotation or you want to create a new one.
logMsg exception: /tappas.log (Read-only file system)15:32 - Process Input Data script is running...
logMsg exception: /tappas.log (Read-only file system)15:32 - [ERROR] Invalid annotation line (invalid character used for ID). Line number: 14.
chrX novel_isoform transcript 6544275 6549502 . + . ID=ESPRESSO:chrX:34697:0;Parent=ENSMUSG00000068270.16;gene_id=ENSMUSG00000068270.16;transcript_id=ESPRESSO:chrX:34697:0
logMsg exception: /tappas.log (Read-only file system)15:32 - Closing project 'islet BKO'

Line 14 is the first time a novel_isoform occurs in the GFF3 file. What is the invalid character used for ID? The GFF3 file is a little different from the format shown in the overview.

Thanks, Nick

[carolinamonzo]

Hi Nick,

Unfortunately TappAS uses a GFF3-like file, not a classical GFF3. If you want to use your espresso files, you need to format them in the same way as we have in the overview.

Another option could be to pass the .gtf from espresso through IsoAnnot so you can annotate it and have the output gff3 directly in tappAS format.

Best wishes,
Carolina.

[nick-webster]

OK. Thanks for the suggestion. I’ll try passing it through IsoAnnot. Nick **************************************************************** Nicholas Webster, Ph.D., M.A. Professor of Medicine Chief, Division of Endocrinology and Metabolism University of California, San Diego 9500 Gilman Drive La Jolla CA 92093 (858) 534-6275

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On Nov 21, 2025, at 12:32 AM, Carolina Monzó ***@***.***> wrote: carolinamonzo left a comment (ConesaLab/tappAS#67) <https://urldefense.com/v3/__https://github.com/ConesaLab/tappAS/issues/67*issuecomment-3561966983__;Iw!!LLK065n_VXAQ!j_4P2bZ1h26cR-VEbzXkWmYg1cEMn5-SjSiE7q1hDEg6uO3OwqL5EqUG9q8qIrl2InwrgVME1QDN45_V9JAHer8Hhms$> Hi Nick, Unfortunately TappAS uses a GFF3-like file, not a classical GFF3. If you want to use your espresso files, you need to format them in the same way as we have in the overview. Another option could be to pass the .gtf from espresso through IsoAnnot so you can annotate it and have the output gff3 directly in tappAS format. Best wishes, Carolina. — Reply to this email directly, view it on GitHub <https://urldefense.com/v3/__https://github.com/ConesaLab/tappAS/issues/67*issuecomment-3561966983__;Iw!!LLK065n_VXAQ!j_4P2bZ1h26cR-VEbzXkWmYg1cEMn5-SjSiE7q1hDEg6uO3OwqL5EqUG9q8qIrl2InwrgVME1QDN45_V9JAHer8Hhms$>, or unsubscribe <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AD3AGXCQOYYR2GTSWDD6PX3353EZXAVCNFSM6AAAAACMYA3ADWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTKNRRHE3DMOJYGM__;!!LLK065n_VXAQ!j_4P2bZ1h26cR-VEbzXkWmYg1cEMn5-SjSiE7q1hDEg6uO3OwqL5EqUG9q8qIrl2InwrgVME1QDN45_V9JAHCXhzr7Y$>. You are receiving this because you authored the thread.

[nick-webster]

Hi Carolina, I managed to run the annotation file through IsoAnnotLite and got a gff3 file. But I run into a problem with Tappas. When I start the program it tries to download R packages but fails:

2025-11-21 Fri 13:38
13:38:31.728460 - tappas 1.1.1 using Java 24.0.1+4
logMsg exception: /tappas.log (Read-only file system)13:38 - Available CPUs for JVM: 16
logMsg exception: /tappas.log (Read-only file system)13:38 - Available memory for JVM: 24.00 GB
logMsg exception: /tappas.log (Read-only file system)13:38 - Setting Rscript full file path to: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/bin
logMsg exception: /tappas.log (Read-only file system)13:38 - Setting Rscript full file path to: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/bin
logMsg exception: /tappas.log (Read-only file system)13:38 - [WARN] Unable to get Rscript version: Cannot run program "Rscript": error=2, No such file or directory
WARNING: You must have Rscript installed and in your environment path.
logMsg exception: /tappas.log (Read-only file system)13:38 - Setting Rscript full file path to: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/bin
logMsg exception: /tappas.log (Read-only file system)13:38 - [WARN] Unable to get R packages: Cannot run program "Rscript": error=2, No such file or directory
logMsg exception: /tappas.log (Read-only file system)13:38 - Setting Rscript full file path to: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/bin
logMsg exception: /tappas.log (Read-only file system)13:38 - [WARN] Unable to get R packages: Cannot run program "Rscript": error=2, No such file or directory
logMsg exception: /tappas.log (Read-only file system)13:38 - [ERROR] The installation didn't work correctly.
logMsg exception: /tappas.log (Read-only file system)

I have all the packages already installed manually and using the source so I ignored warnings and tried the demo:

logMsg exception: /tappas.log (Read-only file system)13:51 - The custom annotation file has been modified. We are going to load the version you used to create the project.
logMsg exception: /tappas.log (Read-only file system)13:51 - Annotation loaded correctly. Check if the project contains the correct annotation or you want to create a new one.
logMsg exception: /tappas.log (Read-only file system)13:51 - Input Data dialog results: tappas.DlgInputData$Params@57cdedb
logMsg exception: /tappas.log (Read-only file system)13:51 - Process Input Data script is running...
logMsg exception: /tappas.log (Read-only file system)13:51 - Checking design file: /Users/nickwebster/tappasWorkspace/References/Mus_musculus/Demo/1/experimental_design.tsv
logMsg exception: /tappas.log (Read-only file system)13:51 - Design file passed initial check.
logMsg exception: /tappas.log (Read-only file system)13:51 - Checking specified matrix file (Two_Group_Comparison): /Users/nickwebster/tappasWorkspace/References/Mus_musculus/Demo/1/expression_matrix.tsv
logMsg exception: /tappas.log (Read-only file system)13:51 - Matrix file passed initial check.
logMsg exception: /tappas.log (Read-only file system)13:51 - Processing expression matrix file: /Users/nickwebster/tappasWorkspace/References/Mus_musculus/Demo/1/expression_matrix.tsv...
logMsg exception: /tappas.log (Read-only file system)13:51 - Experiment type: Two-Group Comparison
logMsg exception: /tappas.log (Read-only file system)13:51 - Matrix has 2 experimental groups with a total of 4 samples.
logMsg exception: /tappas.log (Read-only file system)13:51 - Sample column mapping: 1, 2, 3, 4
logMsg exception: /tappas.log (Read-only file system)13:51 - Expression matrix file processing completed.
logMsg exception: /tappas.log (Read-only file system)13:51 - Writing expression matrix factors file to /Users/nickwebster/tappasWorkspace/Projects/Project.548610896.tappas/InputData/exp_factors.txt
logMsg exception: /tappas.log (Read-only file system)13:51 - Generated expression matrix factors file in 0 ms
logMsg exception: /tappas.log (Read-only file system)13:51 - Writing time course factors file to /Users/nickwebster/tappasWorkspace/Projects/Project.548610896.tappas/Data/time_factors.txt
logMsg exception: /tappas.log (Read-only file system)13:51 - Generated time factors file in 2 ms
logMsg exception: /tappas.log (Read-only file system)13:51 - Filtering/normalizing expression matrix...
logMsg exception: /tappas.log (Read-only file system)13:51 - Matrix script: /var/folders/v9/tzx_rfsn28v2znvg94csf24m0000gn/T/tappas16585901340359089696.R
logMsg exception: /tappas.log (Read-only file system)13:51 - Rscript: Rscript
logMsg exception: /tappas.log (Read-only file system)13:51 - Running ExpMatrix filter/normalization script:
[Rscript, /var/folders/v9/tzx_rfsn28v2znvg94csf24m0000gn/T/tappas16585901340359089696.R, /Users/nickwebster/tappasWorkspace/Projects/Project.548610896.tappas/InputData/input_matrix.tsv, /Users/nickwebster/tappasWorkspace/Projects/Project.548610896.tappas/InputData/exp_factors.txt, /Users/nickwebster/tappasWorkspace/References/Mus_musculus/Demo/1/transcript_lengths.tsv, /Users/nickwebster/tappasWorkspace/Projects/Project.548610896.tappas/InputData/input_normalized_matrix.tsv, 1.0, 100.0, Y]
logMsg exception: /tappas.log (Read-only file system)13:51 - [ERROR] Unable to run Input matrix Filter/Normalization script: Cannot run program "Rscript": error=2, No such file or directory
logMsg exception: /tappas.log (Read-only file system)13:51 - [ERROR] Unable to filter/normalize expression matrix.
logMsg exception: /tappas.log (Read-only file system)13:51 - Closing project 'demo'
logMsg exception: /tappas.log (Read-only file system)

Again it seems the program cannot run an Rscript. But Rscript is present at the location specified by the path. I don't know why the program can't call Rscript.

Any ideas? Thanks, Nick

[carolinamonzo]

Hi Nick,

Are you running it in a Windows computer? If that's the case, the path to the Rscript should end with Rscript.exe. If you are working on a linux, it's very strange, the problem is that until tappAS finds R and Rscript installed in the path that you have specified (/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/bin), and it has access to the installed packages, it won't run.

Can you tell me about the computer you are using, and what is written inside the file "your_path/tappAS_workdir/tappasWorkspace/App/rscript_path.txt"?

Best wishes,
Carolina.

[nick-webster]

Hi Carolina, I am running it on an Intel-based Mac under OSX 15.6.1. The script_path.txt contains /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/bin I checked and there are copies of Rscript and R in the /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/bin directory. I opened a terminal in the bin directory and looked at the versions installed: (base) ***@***.*** bin % R --version R version 4.2.3 (2023-03-15) -- "Shortstop Beagle" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin13.4.0 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under the terms of the GNU General Public License versions 2 or 3. For more information about these matters see https://www.gnu.org/licenses/. (base) ***@***.*** bin % Rscript --version Rscript (R) version 4.2.3 (2023-03-15) R seems to run OK if I open it in that directory: (base) ***@***.*** bin % R R version 4.2.3 (2023-03-15) -- "Shortstop Beagle" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin13.4.0 (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.

q()

Not sure why tappAS is unable to run R and Rscript if it is being pointed to this directory. I could point the script.txt file to a different R and Rscript installation. They are also installed in a number of conda environments as well as the Applications folder. Thanks, Nick **************************************************************** Nicholas Webster, Ph.D., M.A. Professor of Medicine Chief, Division of Endocrinology and Metabolism University of California, San Diego 9500 Gilman Drive La Jolla CA 92093 (858) 534-6275

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On Nov 24, 2025, at 4:13 AM, Carolina Monzó ***@***.***> wrote: carolinamonzo left a comment (ConesaLab/tappAS#67) <https://urldefense.com/v3/__https://github.com/ConesaLab/tappAS/issues/67*issuecomment-3570498494__;Iw!!LLK065n_VXAQ!mN5ddMCDDY_V4PGqng6t9K1VpLCfP0TW2sFiywoeED1VAUvHDiR8Lqmd3v8Z6zuATcHZiEmbi3Q1ejEY-8YYREBbzhA$> Hi Nick, Are you running it in a Windows computer? If that's the case, the path to the Rscript should end with Rscript.exe. If you are working on a linux, it's very strange, the problem is that until tappAS finds R and Rscript installed in the path that you have specified (/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/bin), and it has access to the installed packages, it won't run. Can you tell me about the computer you are using, and what is written inside the file "your_path/tappAS_workdir/tappasWorkspace/App/rscript_path.txt"? Best wishes, Carolina. — Reply to this email directly, view it on GitHub <https://urldefense.com/v3/__https://github.com/ConesaLab/tappAS/issues/67*issuecomment-3570498494__;Iw!!LLK065n_VXAQ!mN5ddMCDDY_V4PGqng6t9K1VpLCfP0TW2sFiywoeED1VAUvHDiR8Lqmd3v8Z6zuATcHZiEmbi3Q1ejEY-8YYREBbzhA$>, or unsubscribe <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AD3AGXEXCVGRPE5SWM7CJ4336LY7RAVCNFSM6AAAAACMYA3ADWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTKNZQGQ4TQNBZGQ__;!!LLK065n_VXAQ!mN5ddMCDDY_V4PGqng6t9K1VpLCfP0TW2sFiywoeED1VAUvHDiR8Lqmd3v8Z6zuATcHZiEmbi3Q1ejEY-8YYOIzSo1g$>. You are receiving this because you authored the thread.

[nick-webster]

Hi Carolina, I wondered if you had any ideas to get tapers to run Rscript? It runs fine if I call R in terminal using the rscript_path.txt information. So why doesn't tappas call R?

Nick

[carolinamonzo]

Hi Nick, honestly I'm out of ideas, I'm tagging in @julensantiago, the last person who worked on tappAS to see if he can jump in.

[julensantiago]

Hi Nick,

Thanks for providing the detailed logs.

I think the issue is that the configuration file requires the full path including the executable name, not just the directory where it resides. Since the file is currently pointing to the folder (.../bin), tappAS cannot execute the script.

Please modify the content of your rscript_path.txt to include the binary name at the end:

/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/bin/Rscript

Once you save the file with this full path, please restart tappAS if it is currently open for the changes to take effect. It should then be able to launch R correctly.

Let me know if this works for you!

Best wishes,
Julen.

[nick-webster]

Hi Julen, I have the rscript_path.txt file exactly as you suggest but Tappas still can’t run R Here’s the log after starting Tappas. It was not able to download the resources. 2025-12-09 Tue 11:52 11:52:53.949513 - tappas 1.1.1 using Java 24.0.1+4 logMsg exception: /tappas.log (Read-only file system)11:52 - Available CPUs for JVM: 16 logMsg exception: /tappas.log (Read-only file system)11:52 - Available memory for JVM: 24.00 GB logMsg exception: /tappas.log (Read-only file system)11:52 - Setting Rscript full file path to: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/bin/Rscript logMsg exception: /tappas.log (Read-only file system)11:52 - Setting Rscript full file path to: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/bin/Rscript logMsg exception: /tappas.log (Read-only file system)11:52 - [WARN] Unable to get Rscript version: Cannot run program "Rscript": error=2, No such file or directory WARNING: You must have Rscript installed and in your environment path. logMsg exception: /tappas.log (Read-only file system)11:52 - Setting Rscript full file path to: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/bin/Rscript logMsg exception: /tappas.log (Read-only file system)11:52 - [WARN] Unable to get R packages: Cannot run program "Rscript": error=2, No such file or directory logMsg exception: /tappas.log (Read-only file system)11:53 - Setting Rscript full file path to: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/bin/Rscript logMsg exception: /tappas.log (Read-only file system)11:53 - [WARN] Unable to get R packages: Cannot run program "Rscript": error=2, No such file or directory logMsg exception: /tappas.log (Read-only file system)11:53 - [ERROR] The installation didn't work correctly. logMsg exception: /tappas.log (Read-only file system) If I open that bin directory in Terminal and run Rscript I get: (base) ***@***.*** bin % Rscript Usage: Rscript [options] file [args] or: Rscript [options] -e expr [-e expr2 ...] [args] A binary front-end to R, for use in scripting applications. Options: --help Print usage and exit --version Print version and exit --verbose Print information on progress --default-packages=LIST Attach these packages on startup; a comma-separated LIST of package names, or 'NULL' and options to R (in addition to --no-echo --no-restore), for example: --save Do save workspace at the end of the session --no-environ Don't read the site and user environment files --no-site-file Don't read the site-wide Rprofile --no-init-file Don't read the user R profile --restore Do restore previously saved objects at startup --vanilla Combine --no-save, --no-restore, --no-site-file, --no-init-file and --no-environ Expressions (one or more '-e <expr>') may be used *instead* of 'file'. Any additional 'args' can be accessed from R via 'commandArgs(TRUE)'. See also ?Rscript from within R. (base) ***@***.*** bin % Rscript --version Rscript (R) version 4.2.3 (2023-03-15) So Rscript is there and functional. Could it be a permission issue? The resource_v1.1.1.txt file is empty. Should that have a directory where resources can be found? Thanks, Nick **************************************************************** Nicholas Webster, Ph.D., M.A. Professor of Medicine Chief, Division of Endocrinology and Metabolism University of California, San Diego 9500 Gilman Drive La Jolla CA 92093 (858) 534-6275

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On Dec 9, 2025, at 2:22 AM, julensantiago ***@***.***> wrote: julensantiago left a comment (ConesaLab/tappAS#67) <https://urldefense.com/v3/__https://github.com/ConesaLab/tappAS/issues/67*issuecomment-3631449350__;Iw!!LLK065n_VXAQ!nBspK269nIS2BkVg_FGmeTdR-DxE2taFm_7M8u-jbT3mD0DmOdGcvZiSXm6lAe-2pz5_SttdZT_Th2xrDLNmLwvVn-k$> Hi Nick, Thanks for providing the detailed logs. I think the issue is that the configuration file requires the full path including the executable name, not just the directory where it resides. Since the file is currently pointing to the folder (.../bin), tappAS cannot execute the script. Please modify the content of your rscript_path.txt to include the binary name at the end: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/bin/Rscript Once you save the file with this full path, please restart tappAS if it is currently open for the changes to take effect. It should then be able to launch R correctly. Let me know if this works for you! Best wishes, Julen. — Reply to this email directly, view it on GitHub <https://urldefense.com/v3/__https://github.com/ConesaLab/tappAS/issues/67*issuecomment-3631449350__;Iw!!LLK065n_VXAQ!nBspK269nIS2BkVg_FGmeTdR-DxE2taFm_7M8u-jbT3mD0DmOdGcvZiSXm6lAe-2pz5_SttdZT_Th2xrDLNmLwvVn-k$>, or unsubscribe <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AD3AGXDVQAK5KHIYZXU6AED4A2PEXAVCNFSM6AAAAACMYA3ADWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTMMZRGQ2DSMZVGA__;!!LLK065n_VXAQ!nBspK269nIS2BkVg_FGmeTdR-DxE2taFm_7M8u-jbT3mD0DmOdGcvZiSXm6lAe-2pz5_SttdZT_Th2xrDLNmv7dmaAM$>. You are receiving this because you authored the thread.

[julensantiago]

Hi Nick,

Thanks for the update.

I suspect two things might be happening here:

1. Global execution: Even if you are inside the folder, running Rscript in the terminal usually executes the global installation (via the PATH variable) rather than the local file. This gives a false positive, making it look like the local file is working when the terminal is actually using the global one.
2. Version mismatch: You are in a 4.5-x86_64 folder, but the output says R version 4.2.3. We need to confirm that the Rscript binary actually exists inside that specific 4.5 folder and that it is a valid executable, as the versions don't match.
   To verify the correct path for the config file, could you please run these two commands in terminal?

which Rscript

To see where the active Rscript is actually running from, and:

ls -l /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/bin/Rscript

To confirm if the Rscript binary physically exists at that specific path.

If these checks don't help us identify the error, please let me know and I will investigate further.

Best wishes,
Julen

[nick-webster]

Hi Julen, You are correct that the Rscript called is in PATH /Users/nickwebster/anaconda3/bin/Rscript This is version 4.2.3. If I check the Rscript in /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/bin/Rscript it is version 4.5.1 ***@***.*** bin % ./Rscript --version Rscript (R) version 4.5.1 (2025-06-13) (base) ***@***.*** bin % ls -l /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/bin/Rscript -rwxrwxr-x@ 1 root admin 70944 Jun 13 18:46 /Library/Frameworks/R.framework/Versions/4.5-x So here is a functional Rscript in that directory but it is not being called. I changed the rscript_path.txt file to read /Users/nickwebster/anaconda3/bin/Rscript same as the one called in PATH but the program has the same error 2025-12-11 Thu 11:20 11:20:50.344912 - tappas 1.1.1 using Java 24.0.1+4 logMsg exception: /tappas.log (Read-only file system)11:20 - Available CPUs for JVM: 16 logMsg exception: /tappas.log (Read-only file system)11:20 - Available memory for JVM: 24.00 GB logMsg exception: /tappas.log (Read-only file system)11:20 - Setting Rscript full file path to: /Users/nickwebster/anaconda3/bin/Rscript logMsg exception: /tappas.log (Read-only file system)11:20 - Setting Rscript full file path to: /Users/nickwebster/anaconda3/bin/Rscript logMsg exception: /tappas.log (Read-only file system)11:20 - [WARN] Unable to get Rscript version: Cannot run program "Rscript": error=2, No such file or directory WARNING: You must have Rscript installed and in your environment path. logMsg exception: /tappas.log (Read-only file system)11:20 - Setting Rscript full file path to: /Users/nickwebster/anaconda3/bin/Rscript logMsg exception: /tappas.log (Read-only file system)11:20 - [WARN] Unable to get R packages: Cannot run program "Rscript": error=2, No such file or directory logMsg exception: /tappas.log (Read-only file system)11:20 - Setting Rscript full file path to: /Users/nickwebster/anaconda3/bin/Rscript logMsg exception: /tappas.log (Read-only file system)11:20 - [WARN] Unable to get R packages: Cannot run program "Rscript": error=2, No such file or directory logMsg exception: /tappas.log (Read-only file system)11:20 - [ER (base) ***@***.*** bin % ls -l /Users/nickwebster/anaconda3/bin/Rscript -rwxr-xr-x 1 nickwebster staff 13512 Nov 13 10:34 /Users/nickwebster/anaconda3/bin/Rscript Any thoughts why it might be failing? Nick **************************************************************** Nicholas Webster, Ph.D., M.A. Professor of Medicine Chief, Division of Endocrinology and Metabolism University of California, San Diego 9500 Gilman Drive La Jolla CA 92093 (858) 534-6275

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On Dec 10, 2025, at 1:29 AM, julensantiago ***@***.***> wrote: julensantiago left a comment (ConesaLab/tappAS#67) <https://urldefense.com/v3/__https://github.com/ConesaLab/tappAS/issues/67*issuecomment-3636156077__;Iw!!LLK065n_VXAQ!jtotXKYmv3r1fOTr05LEu07PF2784pLiEaE_RbH0BvpBpzAHCbfFNcQ4nnWwpnCOry4S9l7eb-SJjA23k28X0e4ZTM8$> Hi Nick, Thanks for the update. I suspect two things might be happening here: Global execution: Even if you are inside the folder, running Rscript in the terminal usually executes the global installation (via the PATH variable) rather than the local file. This gives a false positive, making it look like the local file is working when the terminal is actually using the global one. Version mismatch: You are in a 4.5-x86_64 folder, but the output says R version 4.2.3. We need to confirm that the Rscript binary actually exists inside that specific 4.5 folder and that it is a valid executable, as the versions don't match. To verify the correct path for the config file, could you please run these two commands in terminal? which Rscript To see where the active Rscript is actually running from, and: ls -l /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/bin/Rscript To confirm if the Rscript binary physically exists at that specific path. If these checks don't help us identify the error, please let me know and I will investigate further. Best wishes, Julen — Reply to this email directly, view it on GitHub <https://urldefense.com/v3/__https://github.com/ConesaLab/tappAS/issues/67*issuecomment-3636156077__;Iw!!LLK065n_VXAQ!jtotXKYmv3r1fOTr05LEu07PF2784pLiEaE_RbH0BvpBpzAHCbfFNcQ4nnWwpnCOry4S9l7eb-SJjA23k28X0e4ZTM8$>, or unsubscribe <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AD3AGXDTOKQM6WMAC75XX7T4A7RYZAVCNFSM6AAAAACMYA3ADWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTMMZWGE2TMMBXG4__;!!LLK065n_VXAQ!jtotXKYmv3r1fOTr05LEu07PF2784pLiEaE_RbH0BvpBpzAHCbfFNcQ4nnWwpnCOry4S9l7eb-SJjA23k28X_-40THY$>. You are receiving this because you authored the thread.

[julensantiago]

Hi Nick,

Looking at the logs and the application structure, it appears the root cause is indeed the Read-only file system error.

This probably indicates that macOS is running TappAS in "App Translocation" mode (a security sandbox for apps downloaded from the internet), which prevents it from writing logs, creating the workspace, and executing external tools like Rscript.

Since you downloaded a ZIP file, the system automatically applies a quarantine flag to the unzipped application if it remains in the Downloads folder.

To fix this, please follow these steps:

1. Locate the App: Go to your Downloads folder (or wherever you unzipped the file) and locate the tappAS.app icon.

2. Remove Quarantine: Open your Terminal and run the following command to grant the necessary permissions:

xattr -r -d com.apple.quarantine /path/to/your/tappAS.app

Close the app if it's open and launch it again. The read-only errors should disappear, and it should be able to execute the Rscript.

Let me know if this works for you!

Best regards,

Julen

[nick-webster]

Hi Julen, Unfortunately, that did not solve the problem. I tried changing permissions in terminal and also moving app to Applications (which should also fix the security problem) but still get the same error. 2025-12-16 Tue 14:25 14:25:38.250700 - tappas 1.1.1 using Java 24.0.1+4 logMsg exception: /tappas.log (Read-only file system)14:25 - Available CPUs for JVM: 16 logMsg exception: /tappas.log (Read-only file system)14:25 - Available memory for JVM: 24.00 GB logMsg exception: /tappas.log (Read-only file system)14:25 - Setting Rscript full file path to: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/bin/Rscript logMsg exception: /tappas.log (Read-only file system)14:25 - Setting Rscript full file path to: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/bin/Rscript logMsg exception: /tappas.log (Read-only file system)14:25 - [WARN] Unable to get Rscript version: Cannot run program "Rscript": error=2, No such file or directory WARNING: You must have Rscript installed and in your environment path. logMsg exception: /tappas.log (Read-only file system)14:25 - Setting Rscript full file path to: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/bin/Rscript logMsg exception: /tappas.log (Read-only file system)14:25 - [WARN] Unable to get R packages: Cannot run program "Rscript": error=2, No such file or directory logMsg exception: /tappas.log (Read-only file system)14:25 - Setting Rscript full file path to: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/bin/Rscript logMsg exception: /tappas.log (Read-only file system)14:25 - [WARN] Unable to get R packages: Cannot run program "Rscript": error=2, No such file or directory logMsg exception: /tappas.log (Read-only file system)14:25 - [ERROR] The installation didn't work correctly. logMsg exception: /tappas.log (Read-only file system) Opening R console or R studio opens the R instance at /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/bin/ so the program, is installed there correctly. Or running ./Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/bin/Rscript works. This has me puzzled. Thanks, Nick **************************************************************** Nicholas Webster, Ph.D., M.A. Professor of Medicine Chief, Division of Endocrinology and Metabolism University of California, San Diego 9500 Gilman Drive La Jolla CA 92093 (858) 534-6275

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On Dec 16, 2025, at 7:47 AM, julensantiago ***@***.***> wrote: julensantiago left a comment (ConesaLab/tappAS#67) <https://urldefense.com/v3/__https://github.com/ConesaLab/tappAS/issues/67*issuecomment-3661213254__;Iw!!LLK065n_VXAQ!hem0J6ae8AHKGTe4uNd6ICcinX39z7KsxTzx8e9s7JUBbmYbD6pEDla1L0BcTjzPUOKjIGu5UKo_XhzpVS4K0SVJRXI$> Hi Nick, Looking at the logs and the application structure, it appears the root cause is indeed the Read-only file system error. This probably indicates that macOS is running TappAS in "App Translocation" mode (a security sandbox for apps downloaded from the internet), which prevents it from writing logs, creating the workspace, and executing external tools like Rscript. Since you downloaded a ZIP file, the system automatically applies a quarantine flag to the unzipped application if it remains in the Downloads folder. To fix this, please follow these steps: Locate the App: Go to your Downloads folder (or wherever you unzipped the file) and locate the tappAS.app icon. Remove Quarantine: Open your Terminal and run the following command to grant the necessary permissions: xattr -r -d com.apple.quarantine /path/to/your/tappAS.app Close the app if it's open and launch it again. The read-only errors should disappear, and it should be able to execute the Rscript. Let me know if this works for you! Best regards, Julen — Reply to this email directly, view it on GitHub <https://urldefense.com/v3/__https://github.com/ConesaLab/tappAS/issues/67*issuecomment-3661213254__;Iw!!LLK065n_VXAQ!hem0J6ae8AHKGTe4uNd6ICcinX39z7KsxTzx8e9s7JUBbmYbD6pEDla1L0BcTjzPUOKjIGu5UKo_XhzpVS4K0SVJRXI$>, or unsubscribe <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AD3AGXFRUZL5Z4TRD7SYGZD4CASR7AVCNFSM6AAAAACMYA3ADWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTMNRRGIYTGMRVGQ__;!!LLK065n_VXAQ!hem0J6ae8AHKGTe4uNd6ICcinX39z7KsxTzx8e9s7JUBbmYbD6pEDla1L0BcTjzPUOKjIGu5UKo_XhzpVS4KBCvzRtk$>. You are receiving this because you authored the thread.

[julensantiago]

Hi Nick,

Thank you for your patience and for trying all the troubleshooting steps.

I have an update: after further investigation, we have confirmed that this is not a configuration error on your side, but rather a bug within the application itself that we have recently detected affecting macOS builds.

Unfortunately, we won't be able to push a fix before the upcoming holiday break, but we will address this issue when we return.

Workaround: If you need to use the tool urgently, the application is functional on Linux. I would recommend setting up a Linux Virtual Machine (e.g., using VirtualBox on your Mac) to run your analysis in the meantime.

Apologies for the inconvenience and the time spent debugging this.

Happy holidays,

Julen