Remote server down

[Mosharghi]

I've been trying to install BulkSignalR package and I still can't because of this error:

✖ Remote server is down.
"https://partage-dev.montp.inserm.fr:9192/CBSB/"
Error: package or namespace load failed for ‘BulkSignalR’:
.onLoad failed in loadNamespace() for 'BulkSignalR', details:
call: .testRemoteServer()
error:
Error: loading failed
Execution halted
ERROR: loading failed
Installation goes to the very end and then with this error everything stops.
Can you guys please look at this issue?
Many thanks,
Mohammadreza Sharghi.

[jcolinge]

Dear Dr Sharghi, Please try again, it can be that the web server from which databases are downloaded was down. I have just tested it and it seems OK. Best regards, Jacques Colinge

…

________________________________ De : Mosharghi ***@***.***> Envoyé : mercredi 17 décembre 2025 21:31 À : jcolinge/BulkSignalR Cc : Subscribed Objet : [jcolinge/BulkSignalR] Remote server down (Issue #17) [https://avatars.githubusercontent.com/u/189032299?s=20&v=4]Mosharghi created an issue (jcolinge/BulkSignalR#17)<#17> I've been trying to install BulkSignalR package and I still can't because of this error: ✖ Remote server is down. "https://partage-dev.montp.inserm.fr:9192/CBSB/" Error: package or namespace load failed for ‘BulkSignalR’: .onLoad failed in loadNamespace() for 'BulkSignalR', details: call: .testRemoteServer() error: Error: loading failed Execution halted ERROR: loading failed Installation goes to the very end and then with this error everything stops. Can you guys please look at this issue? Many thanks, Mohammadreza Sharghi. — Reply to this email directly, view it on GitHub<#17>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/APWZSTCB7WQU5MMW6XXD54T4CG4QJAVCNFSM6AAAAACPLK35X2VHI2DSMVQWIX3LMV43ASLTON2WKOZTG42DAMZVGY4DKMY>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[Mosharghi]

I think the internet I was using, has blocked the connection. Thank you so much, now it's working at home.
Is there any way to connect without being blocked by firwall or stuff like that?
Best,
Mohammadreza.

[jcolinge]

Dear Mohammadreza, You need the connection on the first time to get the databases. Afterwards, you can work offline unless you explicitly ask for an update. Best, Jacques Le 18/12/2025 à 13:59, Mosharghi a écrit :

…

*Mosharghi* left a comment (jcolinge/BulkSignalR#17) <#17 (comment)> I think the internet I was using, has blocked the connection. Thank you so much, now it's working at home. Is there any way to connect without being blocked by firwall or stuff like that? Best, Mohammadreza. — Reply to this email directly, view it on GitHub <#17 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/APWZSTDIORNV5XNHZME3AVT4CKQLFAVCNFSM6AAAAACPLK35X2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTMNZQGE3TGNJYGY>. You are receiving this because you commented.Message ID: ***@***.***>

-- Jacques Colinge, PhD, Professor Cancer Bioinformatics and Systems Biology Institut de Recherche en Cancérologie de Montpellier Inserm U1194 - Université de Montpellier Faculté de Médecine - ICM Val d'Aurelle Campus Val d’Aurelle 208 rue des Apothicaires F-34298 Montpellier Cedex 5, France Tel : +33 (0)411 283118 FAX : +33 (0)467 613787 E-mail ***@***.*** Web :http://www.ircm.fr

[Mosharghi]

Dear Jacques,
It worked finally, thank you very much for all the guidance.
Sincerely,
Mohammadreza.

[ycao6928]

Dear Jacques,

I also encountered this issue. I can indeed access the "https://partage-dev.montp.inserm.fr:9192/CBSB/" website on the my browser but somehow it still shows the server is down when installing the package. Would you happen to know more on this ?

Best regards,
Yue

devtools::install_github("jcolinge/BulkSignalR",build_vignettes = FALSE)
Downloading GitHub repo jcolinge/BulkSignalR@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All
2: CRAN packages only
3: None
4: xfun (0.54 -> 0.55) [CRAN]
5: knitr (1.50 -> 1.51) [CRAN]

Enter one or more numbers, or an empty line to skip updates:
Installing 2 packages: BulkSignalR, SingleCellSignalR
Installing packages into ‘/enna/nobackup/biostat/Rpackages/v4’
(as ‘lib’ is unspecified)
trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/BulkSignalR_1.2.1.tar.gz'
trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/SingleCellSignalR_2.0.1.tar.gz'

• installing source package ‘BulkSignalR’ ...
  ** this is package ‘BulkSignalR’ version ‘1.2.1’
  ** package ‘BulkSignalR’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** R
  ** data
  ** 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
  ✖ Remote server is down.
  "https://partage-dev.montp.inserm.fr:9192/CBSB/"
  Error: package or namespace load failed for ‘BulkSignalR’:
  .onLoad failed in loadNamespace() for 'BulkSignalR', details:
  call: .testRemoteServer()
  error:
  Error: loading failed
  Execution halted
  ERROR: loading failed
• removing ‘/enna/nobackup/biostat/Rpackages/v4/BulkSignalR’
  ERROR: dependency ‘BulkSignalR’ is not available for package ‘SingleCellSignalR’
  Perhaps try a variation of:
  install.packages('BulkSignalR')
• removing ‘/enna/nobackup/biostat/Rpackages/v4/SingleCellSignalR’

The downloaded source packages are in
‘/tmp/RtmpTPhisI/downloaded_packages’
── R CMD build ─────────────────────────────────────────────────────────────────────────
✔ checking for file ‘/tmp/RtmpTPhisI/remotes2ff144652abfd8/jcolinge-BulkSignalR-2b4ade3/DESCRIPTION’ (673ms)
─ preparing ‘BulkSignalR’:
✔ checking DESCRIPTION meta-information
─ checking for LF line-endings in source and make files and shell scripts (350ms)
─ checking for empty or unneeded directories
─ looking to see if a ‘data/datalist’ file should be added
NB: this package now depends on R (>= 4.1.0)
WARNING: Added dependency on R >= 4.1.0 because package code uses the
pipe |> or function shorthand (...) syntax added in R 4.1.0.
File(s) using such syntax:
‘spatial.R’
─ building ‘BulkSignalR_0.0.9.tar.gz’

Installing package into ‘/enna/nobackup/biostat/Rpackages/v4’
(as ‘lib’ is unspecified)
ERROR: dependency ‘SingleCellSignalR’ is not available for package ‘BulkSignalR’
Perhaps try a variation of:
install.packages('SingleCellSignalR')

• removing ‘/enna/nobackup/biostat/Rpackages/v4/BulkSignalR’

[Mosharghi]

@ycao6928: As Jacques mentioned, you have to only download the database just once. You see this error because you have a firewall or internet that blocks your access to the database. I would suggest downloading the database with another internet connection once, and then you can use it with a new connection.

[jcolinge]

Dear Mosharghi,

Thanks for helping. Indeed, the web server must be visible from the R process itself to establish the connection. If it still does not work from a network without firewall or one with appropriate ports open, then I would recommend to try the installation from Bioconductor and not GitHub. The package is included in Bioconductor and it ensures tested releases.

Thanks for our interest in our tool.

Best regards,
Jacques

[Mosharghi]

@jcolinge: No problem at all.
Aside from the database, which was resolved for me, can you please guide us on which inputs are the best for using BulkSignalR?
Are they a raw counts matrix, or normalized counts?
What's your suggestion on this?
I have bulk-normalized counts with gene names, but I was looking for some insights on the input files.
Thank you very much,
Mohammadreza.

[jcolinge]

Sure. You can use both, you just need to specify data were normalized already in case they actually were. Usually, I see no major differences in the results.

Personally, I prefer to give BulkSignalR the raw read counts and let it normalize. Now, if you believe a normalization you would apply at other steps of your project would do good and you want to maintain 100% compatibility, then just give it to BulkSignalR as well.

[Mosharghi]

I see, very good. I will try to feed raw read counts and let BulkSignalR normalize them, and then compare the results.
I can update you on this later.
Thank you very much for your suggestions and responsiveness.
Mohammadreza.