Week 1: Installing R package - Error Screenshots

[DavidRach]

Hello Everyone, as part of the Week #1 material, you will be installing R packages sourced from CRAN, Bioconductor, and GitHub repositories.

While most of these will likely install without any issue, if you encounter an installation error in the process, please take screenshots and attach them in a reply to this post here.

This will help better document the "Troubleshooting Install Errors" section, and also allow us to help walk you through what needs to be done to get the R package to install correctly.

Best Wishes-
David

[inahbianca]

Hello! I got a warning message at the very beginning when trying to install dpylr, and do not know what this means and what to do:

[UMGCCCFCSR]

Hi @inahbianca, this reddit thread had a similar error: https://www.reddit.com/r/Rlanguage/comments/lgs2o3/lib_cusersxxxdocumentsrwinlibrary40_is_not/

Is this your own computer or one for work/school? The next troubleshooting step will depend on that.

For the next step, next to your console, you have the terminal tab, can you type and run the following code

quarto check

Take and share the screenshot of the output and share it, it should look something like this:

I mostly want to make sure that the R installation section is up-to-date.

Thanks!
David

[nina-rozendaal]

I encounter the same problem installing packages I get the error "is not writable".
I wrote "quarto check" in the terminal and the following screenshot is the output, hope you can help me further because now I cannot install anything. Thanks a lot in advance! :)

[UMGCCCFCSR]

@inahbianca and @nina-rozendaal, we were able to get the same error today for one of our in-person participants. There is a popup window that should appear asking whether you want to write to a personal library. Select Yes and the installation proceeded with the install

[iraidatr]

Hi! I'm having problems installing packages from github. Every package I tried to install, I get the same error: cannot open URL. I don't know what's wrong!

[UMGCCCFCSR]

Hi @iraidatr, Before going down the potential solution rabbit-holes, can you follow the troubleshooting steps I suggested in this comment and share the screenshot. I found a reddit thread with a similar error, so depending on what your screenshot shows we have a couple troubleshooting options. Best- David

[iraidatr]

Hi! I found a solution! If I run:
options(download.file.method = "wininet")
before the "install_github(), I can download the package. I think it has something to do with the firewalls that my company uses.

Thank you for your help!

[DavidRach]

That's good to hear @iraidatr! My guess it was trying to access via a particular connection type, so specifying the alternate method as options worked around the issue. Let me know if you encounter similar issues for the other repositories (CRAN or Bioconductor). Best- David

[kushekhar]

I encountered this message in a version control Git tutorial. I cannot push my file to git repo.
Thanks

[UMGCCCFCSR]

Hi @kushekhar, you are in good company, we have quite a few people struggling with this particular step. Hoping to find a solution shortly and update the documentation. Best- David

[UMGCCCFCSR]

Hi @kushekhar, following up in case you are still having an issue. Other users reported following this walkthrough in a new project folder was enough to set up the connection. If still having issues, can you try it and let me know if it works? Thanks - David

[nsenutov]

I was unable to install dplyr:
"loaded via a namespace (and not attached):
[1] compiler_4.5.1 tools_4.5.1

?sessionInfo()
?install.packages()
install.packages("dplyr")
Installing package into ‘C:/Users/nina.senutovitch/AppData/Local/R/win-library/4.5’
(as ‘lib’ is unspecified)
also installing the dependencies ‘lifecycle’, ‘rlang’, ‘vctrs’

There is a binary version available but the source version is later:
binary source needs_compilation
dplyr 1.1.4 1.2.0 TRUE"

[UMGCCCFCSR]

@nsenutov, generally you will have a pop-up window for the binary version but source version later, you will need to click yes on that one. If that still errors out, can you scroll the install text and take a screenshot of the error? Thanks- David

[FabioMambelli]

Hi, I was not able to install somes packages. Here are error messages:

Warning message:
Packages ‘ggcyto’, ‘FlowSOM’, ‘flowGate’ are not available for this version of R

Warning message:
package(s) not installed when version(s) same as or greater than current; use force = TRUE to re-install: 'openCyto' 'CytoML'

Warning message:
In i.p(...) :
installation of package ‘C:/Users/famam/AppData/Local/Temp/RtmpaERXUj/filea9a87b2c4ea8/CytoNorm_2.0.11.tar.gz’ had non-zero exit status

Above is what I retrieve from sessionInfo() function

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Portuguese_Brazil.utf8 LC_CTYPE=Portuguese_Brazil.utf8
[3] LC_MONETARY=Portuguese_Brazil.utf8 LC_NUMERIC=C
[5] LC_TIME=Portuguese_Brazil.utf8

time zone: Europe/Berlin
tzcode source: internal

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] flowSpectrum_0.9.1 ggplot2_4.0.2 flowCore_2.22.1 remotes_2.5.0
[5] PeacoQC_1.20.0 BiocManager_1.30.27 dplyr_1.2.0

loaded via a namespace (and not attached):
[1] gtable_0.3.6 circlize_0.4.17 shape_1.4.6.1
[4] rjson_0.2.23 devtools_2.4.6 GlobalOptions_0.1.3
[7] processx_3.8.6 Biobase_2.70.0 callr_3.7.6
[10] vctrs_0.7.1 tools_4.5.2 ps_1.9.1
[13] generics_0.1.4 stats4_4.5.2 curl_7.0.0
[16] parallel_4.5.2 tibble_3.3.1 flowWorkspace_4.22.1
[19] cluster_2.1.8.1 pkgconfig_2.0.3 data.table_1.18.2.1
[22] RColorBrewer_1.1-3 S7_0.2.1 desc_1.4.3
[25] S4Vectors_0.48.0 graph_1.88.1 lifecycle_1.0.5
[28] compiler_4.5.2 farver_2.1.2 codetools_0.2-20
[31] ComplexHeatmap_2.26.0 clue_0.3-66 usethis_3.2.1
[34] pillar_1.11.1 crayon_1.5.3 ellipsis_0.3.2
[37] cachem_1.1.0 sessioninfo_1.2.3 iterators_1.0.14
[40] foreach_1.5.2 RProtoBufLib_2.22.0 tidyselect_1.2.1
[43] digest_0.6.39 purrr_1.2.1 fastmap_1.2.0
[46] grid_4.5.2 colorspace_2.1-2 cli_3.6.5
[49] magrittr_2.0.4 ncdfFlow_2.56.0 XML_3.99-0.20
[52] pkgbuild_1.4.8 withr_3.0.2 scales_1.4.0
[55] matrixStats_1.5.0 cytolib_2.22.0 png_0.1-8
[58] GetoptLong_1.1.0 memoise_2.0.1 IRanges_2.44.0
[61] doParallel_1.0.17 rlang_1.1.7 glue_1.8.0
[64] Rgraphviz_2.54.0 BiocGenerics_0.56.0 pkgload_1.5.0
[67] R6_2.6.1 fs_1.6.6

[DavidRach]

Nice catch @tomthescientist3001, looks like during my copy-paste-then-edit for the n=20 I forgot to swap the install instructions for the Bioconductor packages in the middle. I will go and swap the code-hint answers on the website to use the correct install function.

[DavidRach]

@FabioMambelli, can you verify your R software version? In the terminal (to the right of the console tab) run the following

quarto check

Take a screenshot of the R installation and version information that is returned.

The 3 packages you listed are Bioconductor packages, Since Bioconductor is currently version 3.22; you might need to upgrade your R installlation to recent version (4.5.0. ?)

[FabioMambelli]

Hi @DavidRach .

This is what returns after quarto check:

PS C:\Users\famam\Documents\RbyMaryland\Week1> quarto check
Quarto 1.8.27
[>] Checking environment information...
Quarto cache location: C:\Users\famam\AppData\Local\quarto
[>] Checking versions of quarto binary dependencies...
Pandoc version 3.6.3: OK
Dart Sass version 1.87.0: OK
Deno version 2.3.1: OK
Typst version 0.13.0: OK
[>] Checking versions of quarto dependencies......OK
[>] Checking Quarto installation......OK
Version: 1.8.27
Path: c:\Users\famam\AppData\Local\Programs\Positron\resources\app\quarto\bin
CodePage: 1252

[>] Checking tools....................OK
TinyTeX: (not installed)
Chromium: (not installed)

[>] Checking LaTeX....................OK
Tex: (not detected)

[>] Checking Chrome Headless....................OK
Using: Chrome found on system
Path: C:\Program Files\Google\Chrome\Application\chrome.exe
Source: Windows Registry

[>] Checking basic markdown render....OK

[>] Checking Python 3 installation....(None)

  Unable to locate an installed version of Python 3.
  Install Python 3 from https://www.python.org/downloads/

[>] Checking R installation...........OK
Version: 4.5.2
Path: C:/PROGRA~1/R/R-4.5.2
LibPaths:
- C:/Users/famam/AppData/Local/R/win-library/4.5
- C:/Program Files/R/R-4.5.2/library
knitr: 1.51
rmarkdown: 2.30

[>] Checking Knitr engine render......OK

PS C:\Users\famam\Documents\RbyMaryland\Week1>

Any idea?

[UMGCCCFCSR]

@FabioMambelli So within the original error:

Not available this version of R: ‘ggcyto’, ‘FlowSOM’, ‘flowGate’

Already installed: 'openCyto' 'CytoML' [don't install these again - David]

Non-zero exit status (ie. failed to install CytoNorm)

Can you run installed.packages() and see any of the 4 (ggcyto, FlowSOM, flowGate, CytoNorm) show up in the list?

You have the most recent version of R installed, so it's not an outdated issue. For the packages that are not listed, I would attempt to reinstall them. The first three are from Bioconductor, so do:

library(BiocManager)
install("ggcyto") 

and repeat this step for the other two

and for CytoNorm use

library(remotes)
install_github("saeyslab/CytoNorm")

Take screenshots of any errors that get returned. Also watch the bottom of your screen in case you have popup windows that require clicks to accept to proceed with the installation

[FabioMambelli]

I think all of them are installed now, because after I loaded them and entered sessionInfo() , i saw this:
other attached packages:
[1] FlowSOM_2.18.0 igraph_2.2.1 CytoNorm_2.0.11 flowGate_1.10.0
[5] ggcyto_1.38.1 ncdfFlow_2.56.0 BH_1.90.0-1 flowWorkspace_4.22.1
[9] flowSpectrum_0.9.1 ggplot2_4.0.2 flowCore_2.22.1 remotes_2.5.0
[13] PeacoQC_1.20.0 BiocManager_1.30.27 dplyr_1.2.0

THanks for the support :D

[sevinji]

Hi, David. The first issue I run into, was that WindowsPowerShell. I have contacted institutional IT to unblock it, not sure how much it affects anything. I have included the screenshot

The second error I run into was installing PeacpQC.

here it is

• DONE (viridisLite)

The downloaded source packages are in
‘C:\Users\sisgandarova\AppData\Local\Temp\Rtmp00eyf4\downloaded_packages’
Warning message:
In file.copy(savedcopy, lib, recursive = TRUE) :
problem copying C:\Users\sisgandarova\AppData\Local\R\win-library\4.5\00LOCK\tibble\libs\x64\tibble.dll to C:\Users\sisgandarova\AppData\Local\R\win-library\4.5\tibble\libs\x64\tibble.dll: Permission denied

[DavidRach]

Hi @sevinji, the second one may also be an issue that IT can fix, it looks like permission is being denied to transfer the unzipped package to its final folder location during the installation process. Keep me updated! Best- David

[kcheah1422]

I didn't necessarily get an error message while attempting to install the dplyr package. It says it was downloaded but I don't see it when I tried sessionInfo()

[UMGCCCFCSR]

Hi @kcheah1422, after install successfull install, you still need to call library() function to have it attached to the local environment. So you would proceed by running library(dplyr) and then run sessionInfo() again to check 😃

[kcheah1422]

Silly me. And thank you! Guess I made the same mistake you did when you were dealing with that RNA-seq data.

[UMGCCCFCSR]

Fortunately we are hear to help you avoid three weeks of head-bashing 🤣

[jessicawoelfel]

I'm probably missing the obvious, but is there a list somewhere of the 20 packages we're supposed to install? Even better if it includes the commands.

[UMGCCCFCSR]

Hi @jessicawoelfel, the list can be found here with the install commands needed available under the drop-down code arrows below each.

[jessicawoelfel]

Thanks!

[katlin-brooke]

I've been able to install all of the R packages except for CytoML which keeps giving me this error:

Thanks in advance!

[DavidRach]

Interesting, I think it might accidentally be trying to use remotes (via devtools wrapper function) to install the package similar to what you would see with install_github().

Can you try the following after closing and reopening your browser (to un-attach any packages current loaded via library and start with a clean slate).

library(BiocManager)
install("CytoML"

Which should hopefully allow it to download.

Alternately, try the :: route to specifically state use BiocManager's install() function.

BiocManager::install("CytoML")
```

Let me know if either works!

Best-
David

[katlin-brooke]

Your first solution did the trick! Thank you!

[amartin270]

Hi David
I'm having trouble installing R packages. For example, when I install dplyr it comes up in the console as "downloaded 1.6 MB", but there is no DONE as is seen in your console. Additionally, when I try to load it by using the library() function, it comes up as this big error message. Am I missing something?

[DavidRach]

Hi @amartin270,

Can you run the following command in the terminal tab and post the screenshot of the output?

quarto check

I think your issue is likely the same one that was encountered in this StackOverFlow post, so we can troubleshoot once we see how the R installation paths are set up.

Best-
David

[amartin270]

Hi David
This is the output when I run that command in the terminal tab. Thanks!

[DavidRach]

Hmm... nothing immediately obvious issue on the path-ing. Could you try reinstalling first rlang, then dplyr (both via install.packages() and then reattempt library(dplyr). If the error repops up, google the first part of the error before it gets to your computers file.path address, and add "R package install error" to the search.

[BethDibnah]

Hi! Not sure if this is an error as I think I was still able to run library(flowCore), and it does appear on my SessionInfo, but wasn't sure what the warning message was, so thought I would share 😊

[DavidRach]

Hi @BethDibnah, you will see this warning when it starts to install, but checks your computer, and already finds the package installed. In this case, it checked the package version for both the local and the one on Bioconductor, found that they were matching, and skipped the installation, keeping the already installed version. So you are all good.

If you had wanted to reinstall completely, you would have incorporated the suggested argument provided in the warning message

library(BiocManager)
install("flowCore", force = TRUE)

Best-
David

[BethDibnah]

Hi David, thanks very much for explaining! That all makes sense, I wasn't sure how I would include the force=true like it suggested but glad it is all good anyways 😊

[Nele-UKE]

**I also had an issue with the library as lib was unspecific... now i get this error after running: > install.packages("usethis")
Can you help me?

Copy of my console:**

install.packages("usethis")
Installing package into ‘/home/nele/R/x86_64-pc-linux-gnu-library/4.3’
(as ‘lib’ is unspecified)
also installing the dependencies ‘credentials’, ‘openssl’, ‘httr2’, ‘curl’, ‘fs’, ‘gert’, ‘gh’

trying URL 'https://cloud.r-project.org/src/contrib/credentials_2.0.3.tar.gz'
Content type 'application/x-gzip' length 283143 bytes (276 KB)

downloaded 276 KB

trying URL 'https://cloud.r-project.org/src/contrib/openssl_2.3.4.tar.gz'
Content type 'application/x-gzip' length 1208445 bytes (1.2 MB)

downloaded 1.2 MB

trying URL 'https://cloud.r-project.org/src/contrib/httr2_1.2.2.tar.gz'
Content type 'application/x-gzip' length 277334 bytes (270 KB)

downloaded 270 KB

trying URL 'https://cloud.r-project.org/src/contrib/curl_7.0.0.tar.gz'
Content type 'application/x-gzip' length 731109 bytes (713 KB)

downloaded 713 KB

trying URL 'https://cloud.r-project.org/src/contrib/fs_1.6.6.tar.gz'
Content type 'application/x-gzip' length 1201011 bytes (1.1 MB)

downloaded 1.1 MB

trying URL 'https://cloud.r-project.org/src/contrib/gert_2.3.1.tar.gz'
Content type 'application/x-gzip' length 130066 bytes (127 KB)

downloaded 127 KB

trying URL 'https://cloud.r-project.org/src/contrib/gh_1.5.0.tar.gz'
Content type 'application/x-gzip' length 46366 bytes (45 KB)

downloaded 45 KB

trying URL 'https://cloud.r-project.org/src/contrib/usethis_3.2.1.tar.gz'
Content type 'application/x-gzip' length 393912 bytes (384 KB)

downloaded 384 KB

• installing source package ‘openssl’ ...
  ** package ‘openssl’ successfully unpacked and MD5 sums checked
  ** using staged installation
  Using PKG_CFLAGS=
  --------------------------- [ANTICONF] --------------------------------
  Configuration failed because openssl was not found. Try installing:
• deb: libssl-dev (Debian, Ubuntu, etc)
• rpm: openssl-devel (Fedora, CentOS, RHEL)
• csw: libssl_dev (Solaris)
• brew: openssl (Mac OSX)
  If openssl is already installed, check that 'pkg-config' is in your
  PATH and PKG_CONFIG_PATH contains a openssl.pc file. If pkg-config
  is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
  R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
  -------------------------- [ERROR MESSAGE] ---------------------------
  tools/version.c:1:10: fatal error: openssl/opensslv.h: No such file or directory
  1 | #include <openssl/opensslv.h>
  | ^~~~~~~~~~~~~~~~~~~~
  compilation terminated.

---

ERROR: configuration failed for package ‘openssl’

• removing ‘/home/nele/R/x86_64-pc-linux-gnu-library/4.3/openssl’
• installing source package ‘curl’ ...
  ** package ‘curl’ successfully unpacked and MD5 sums checked
  ** using staged installation
  Using PKG_CFLAGS=
  Using PKG_LIBS=-lcurl
  --------------------------- [ANTICONF] --------------------------------
  Configuration failed because libcurl was not found. Try installing:
• deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
• rpm: libcurl-devel (Fedora, CentOS, RHEL)
• apk: curl-dev (Alpine)
  If libcurl is already installed, check that 'pkg-config' is in your
  PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
  is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
  R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
  -------------------------- [ERROR MESSAGE] ---------------------------
  :1:10: fatal error: curl/curl.h: No such file or directory
  compilation terminated.

---

ERROR: configuration failed for package ‘curl’

• removing ‘/home/nele/R/x86_64-pc-linux-gnu-library/4.3/curl’
• installing source package ‘fs’ ...
  ** package ‘fs’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** libs
  sh: 1: g++: not found
  g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-FPSnzf/r-base-4.3.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-FPSnzf/r-base-4.3.3=/usr/src/r-base-4.3.3-2build2 -Wdate-time -D_FORTIFY_SOURCE=3 -c dir.cc -o dir.o
  /bin/bash: line 1: g++: command not found
  make: *** [/usr/lib/R/etc/Makeconf:198: dir.o] Error 127
  ERROR: compilation failed for package ‘fs’
• removing ‘/home/nele/R/x86_64-pc-linux-gnu-library/4.3/fs’
  ERROR: dependencies ‘openssl’, ‘curl’ are not available for package ‘credentials’
• removing ‘/home/nele/R/x86_64-pc-linux-gnu-library/4.3/credentials’
  ERROR: dependencies ‘curl’, ‘openssl’ are not available for package ‘httr2’
• removing ‘/home/nele/R/x86_64-pc-linux-gnu-library/4.3/httr2’
  ERROR: dependencies ‘credentials’, ‘openssl’ are not available for package ‘gert’
• removing ‘/home/nele/R/x86_64-pc-linux-gnu-library/4.3/gert’
  ERROR: dependency ‘httr2’ is not available for package ‘gh’
• removing ‘/home/nele/R/x86_64-pc-linux-gnu-library/4.3/gh’
  ERROR: dependencies ‘curl’, ‘fs’, ‘gert’, ‘gh’ are not available for package ‘usethis’
• removing ‘/home/nele/R/x86_64-pc-linux-gnu-library/4.3/usethis’

The downloaded source packages are in
‘/tmp/RtmpSGUced/downloaded_packages’
Warning messages:
1: In install.packages("usethis") :
installation of package ‘openssl’ had non-zero exit status
2: In install.packages("usethis") :
installation of package ‘curl’ had non-zero exit status
3: In install.packages("usethis") :
installation of package ‘fs’ had non-zero exit status
4: In install.packages("usethis") :
installation of package ‘credentials’ had non-zero exit status
5: In install.packages("usethis") :
installation of package ‘httr2’ had non-zero exit status
6: In install.packages("usethis") :
installation of package ‘gert’ had non-zero exit status
7: In install.packages("usethis") :
installation of package ‘gh’ had non-zero exit status
8: In install.packages("usethis") :
installation of package ‘usethis’ had non-zero exit status

[Nele-UKE]

error_releasefile_package´fs.pdf

[DavidRach]

Hi @Nele-UKE , looks like it's just the fs dependency that needs to be fixed in order to get use this to build successfully now.

Try:

install.packages("fs")

Wait for it to error out, and then read through until it tells you what fails. If it is a missing system dependency, install via terminal, then retry installing fs. If it is some other kind of error, screenshot it, and post. We can then look up that particular warning to see if anyone else on the internet has previously encountered it.

Best-
David

[Nele-UKE]

I believe is not a dependency but I am not sure...

/bin/bash: line 1: g++: command not found
make: *** [/usr/lib/R/etc/Makeconf:198: dir.o] Error 127
ERROR: compilation failed for package ‘fs’

• removing ‘/home/nele/R/x86_64-pc-linux-gnu-library/4.3/fs’

What do you think?

[DavidRach]

Hmm.... Maybe this?

sudo apt-get install g++

[Nele-UKE]

Yes I was successful :) Thanks.
I was running in some other issue but I found the solution in the discussions already.

[kcheah1422]

I only have trouble installing the cyCombine package. This is the error message I got.

[DavidRach]

Hi @kcheah1422, it look's like the message you will get when you already have it installed on your system.

Basically, as part of the installation process, it checks to see if it already is present, if it is, it checks the git hash number (1035e320 in this case) is the same for both, and decides to skip the installation since the same version is already present.

You can check to see if cyCombine is already installed using either

installed.packages()

# or

library(cyCombine)

Hope this helps-
David

[kcheah1422]

Awesome, that works! Thanks again for your help.

[Nele-UKE]

I ran into an issue installing PeacoQC ...

This error came up when i try to install png individually:

and when I try install libpng-configI got the error for not available for this R version:

This is my R version:

Any ideas what I can do?

[DavidRach]

Hi @RachaelSheridan, capitol F for "FlowSOM" 😃 Best- David

library(BiocManager)
install("FlowSOM"

[RachaelSheridan]

facepalm I was doing so well too! hahahaha! thank you

[Nele-UKE]

Hmm, so the version is likely Linux Mint working with a particular version in its distro, that is likely fine and we can work around. I just noticed a installation path not writable in the screenshot, can you run the following within Positrons terminal tab and screenshot the output

quarto check

Curious whether it's trying to save the packages to root instead of to an user folder, and running into that kind of issue with sudo

What do you think?

[DavidRach]

Hi @Nele-UKE,

I think I am going to open a separate Discussion thread for your issue (and maybe also download LinuxMint on one of the core laptops to help troubleshoot this one. Did you setup the signing key similar to the outlined process for Debian distros?

Best-
David

[DavidRach]

Hi @Nele-UKE, had a friend try it out on the same Linux Mint with Cinnamon, looks like you are missing a system dependency for the cytolib package.

What you can try is updating these linux system dependencies via your main terminal

sudo apt install libxml2-dev libboost-all-dev libhdf5-dev libprotobuf-dev

At which point you will need to return to Positron and run the following in the console:

remotes::install_github("RGLab/cytolib")

# then if that installs without issues

BiocManager::install("PeacoQC")

If anything errors, send the screenshot.

Best,
David

[tamiimay]

I was successful installing the packages using "pak" package, except for CytoExploreR. Here is what I got:

At first, I thought it could be something related to not attach the GitHub package, so I did it and tried again and got this:

[DavidRach]

Hi @tamiimay, the first screenshot error was due to a typo (missing an l at the end of Hammill).

And the second is expected behavior (troubleshooting the install of the two failing dependencies to get CytoExploreR to work is the hidden challenge for this particular take-home problem 🧰 🔧 ). I'd start by googling to figure out their current repositories.

[nsenutov]

I seem to have lost installed and loaded functions in Positron after a re-start. While I can still load them via the library function, I expected all 20 functions to be viewable via sessionInfo() upon start up. Can you help me figure out what I am missing? Thanks

[DavidRach]

Hi @nsenutov,

Can you see them when you run:

installed.packages()

If no, I will circle back to help troubleshoot.

If yes, they have been properly installed. In a toolbox analogy, you have bought the set of tools from the store and brought them home.

When you call library(), you are opening the toolbox, and placing the tools where you can quickly grab them and use them.

So for example:

library(purrr)
sessionInfo()

You took purrr package out of the toolbox, and have it ready to be used (ie. In reach on the table in the analogy). This is what a loaded and attached package means.

The reason you don't have all 20 packages loaded and attached when reopening Positron, is it would be equivalent of dumping all the toolbox contents in the middle of the table. Yes they would be visible, but it would not be organized, and it might be harder to find a particular tool than it would have been attaching each package individually as needed (due to different packages having functions with same names like select, filter, etc which causes issues)

Best-
David

[nsenutov]

Yes, those I instaled and attaached are visible via installed.packages(), thanks

[SandraLazzaro]

Hi all and nice to e-meet you! Thanks David for organizing this course!
I am still a bit behind, I am setting up my GitHub account and create the repository according to the provided instructions: "You will next create a repository (folder), naming it exactly the same as your username. This will be recognized by GitHub as being a special type of repository corresponding to the ReadMe section of your profile."
I have one question: do I have to select a licence and if yes which one?
Thanks a lot!
Sandra

[DavidRach]

Hi @SandraLazzaro, you don't have to set a license, you can skip it for now and add one later. I will circle back with a short explainer license type resource later. Best- David

[SandraLazzaro]

Thanks David, I did create already the repository with MIT licence as it was in the provided picture. I am trying to remove it but it does not work. Should I remove the created repository and start again or is it ok to leave it like this for now? If I should remove it, could you guide me how to do that?
Thanks,
Sandra

[DavidRach]

Hi @SandraLazzaro, to remove it, you would just need to delete the LICENSE file that will be within the repository. If via the website, click on the particular file, and then find the options on the upper right hand side of the screen if my memory is correct.

[SandraLazzaro]

Thanks! Il mar 10 feb 2026, 1:20 PM David Rach ***@***.***> ha scritto:

…

Hi @SandraLazzaro <https://github.com/SandraLazzaro>, you don't have to set a license, you can skip it for now and add one later. I will circle back with a short explainer license type resource later. Best- David — Reply to this email directly, view it on GitHub <#10 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/B6ERASMM6WXCZLAD6ZFNRYT4LHEJ3AVCNFSM6AAAAACTSCPKWGVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTKNZVGYYTAMQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[FabioMambelli]

How do I know I uploaded the homeworks in the right place? I did not recieve feedback , so I don't know if you guys didn't have time or if I uploaded somewhere wrong.

[FabioMambelli]

I created the folder in the positron and comitted my changes

[DavidRach]

Hi @FabioMambelli , you placed it correctly within the intended Week #1 homework folder, so you indeed place it in the correct location. 🥳

However, it currently only exist within your forked project version (FabioMambelli/CytometryInR). Until a pull-request is submitted proposing the changes to our (UMGCCCFCSR/CytometryInR 's homework branch), I am unaware of the changes, and can't provide feedback on the changes, since they reside entirely within your own project 😃

For the next steps, you would submit a pull request to our homework folder, which opens the review process on my end. See the walk-through for additional details

Best-
David

[Josefinebech]

When I try to install the packages from Github I get this message. What does it mean and how should I proceed?

[DavidRach]

Hi @Josefinebech , message is given when the package is already installed, see #10 (reply in thread) above for full explanation. Best, David

[Stanley-NL]

So I'm catching up on the courses and just did my homework of the week 1 lesson.
All the CARN and github packages get installed without any issues, but for all my Bioconductor packages I get the same message.


So seems like they are downloaded but not properly installed.
Has anyone else run into this and found a solution for it?
I'm already googling it, but so far no luck in finding a solution (except for running it in admin mode, but that's not an option since it's my work PC and I am no admin on it).

[DavidRach]

Hi @Stanley-NL, the error initially appears similar to the one encountered here and here

In the case of those errors, you wouldn't have permissions to write to the software folder resulting in the error, but there would be a pop-up appearing below asking whether you want to set up a personal library (similar to the one seen in the screenshot)

In your case however, you are installing R packages from CRAN, which would likely already be stored in a personal library.

Can you run the following in your console tab:

installed.packages()

Check and see if PeacoQC, flowCore, CytoML and the other Bioconductor packages are listed among installed packages. If so, you are all set, and the likely is just that those four packages (cluster, foreign, lattice, mgcv, and survival) have been denied permission to update, either because they were being actively used, or have some additional install requirement that places them in the system instead of the personal library.

Let me know either way!

Best-
David

[Stanley-NL]

Hi David,

Thanks for the reply.
I tried the installed.packages() function, but then I couldn't find all of the packages, due to reaching the max amount of rows. I'll look into that later to see how I can report all of the data points (or maybe that's something that will pass in one of the future courses).

However instead I tried the find.package() function which was recommened as an alternative for looking up single packages and check most of the Bioconductor packages and got this output:

So, correct me if I'm wrong, but seems that the packages are installed properly and ready to use.

Best-
Stanley

[DavidRach]

Hi @Stanley-NL, good use of find,packages() it looks like they installed correctly. You could also try:

library(dplyr)

library(ggcyto)

Both of these packages will produce messages about loading dependencies or masking functions to the console tab when first loading up, so a good initial check.

Best-
David

[kushekhar]

Hi David, I did actually solve it, partly from the error messages itself and partly from Discussion thread. All is well, up to the W2! Kushi

…

On Sat, Feb 14, 2026 at 15:33 UMGCC FCSR ***@***.***> wrote: Hi @kushekhar <https://github.com/kushekhar>, following up in case you are still having an issue. Other users reported following this walkthrough <https://umgcccfcsr.github.io/CytometryInR/course/00_BonusContent/#not-detecting-git> in a new project folder was enough to set up the connection. If still having issues, can you try it and let me know if it works? Thanks - David — Reply to this email directly, view it on GitHub <#10 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/B5YVUP4FL2K3AKXLQMEFTO34L4W3ZAVCNFSM6AAAAACTSCPKWGVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTKOBQGU2DMMY> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[SandraLazzaro]

Hi David,
I just opened Positron and looks like this, see attached. Any hint?

Thanks,
Sandra

[SandraLazzaro]

Looks like I had to open R and Rstudio? Now I see that

Do I need to sign in with GitHub?
Thank you, Sandra

[DavidRach]

Hi @SandraLazzaro, see our short walkthrough here https://umgcccfcsr.github.io/CytometryInR/course/00_Positron/

Best-
David

[SandraLazzaro]

Thanks David. I have copied now the following URL https://github.com/UMGCCCFCSR/CytometryInR in New Folder from Git and I see this:

Is this correct? Sorry I could not find this part in the walkthrough and... I am also very naive!
Thanks,
Sandra

[UMGCCCFCSR]

Hi Sandra, no worries, start from this portion of the Workstation Setup walkthrough for initial setup: https://umgcccfcsr.github.io/CytometryInR/course/00_WorkstationSetup/Windows.html#connecting-github-and-positron

Best-
David

[jessgeorgex]

Hi David,

I am experiencing this error when attempting to preview my .qmd file. Please could you help me to identify my error?

Thank you!!

[DavidRach]

@jessgeorgex That is a new one to me. It is not happening when you try to install packages regularly via the console, correct? If it is, let me know, there are a couple options we can try to set up the connection.

Within Quarto documents, I will normally separate out the install.packages() lines into their own code chunk, and then set the code-chunk evaluation to false (#| eval: false) so that they are not trying to reinstall R packages everytime I preview/render the document.

Best-
David

[jessgeorgex]

Thank you David, you were right I just needed to stop it from evaluating all of the code. I have now progressed to attempting to install packages from GitHub and am facing this error message:

Any ideas what I'm doing wrong this time? Thank you so much for your help!

[DavidRach]

Hi @jessgeorgex, just confirming that you connected Positron with your GitHub and were are able to pull/push changes without issue? Found a couple potential solutions, but want to make sure what the current git operation status is at. Best- David

[jessgeorgex]

Hi David, Positron is connected to my GitHub, and I was able to pull changes with no issue. When pushing changes I received a 'failed to authenticate', thanks again for your help! Jess.

[liabuffa97]

Hi @DavidRach

Sorry, I’m a couple of steps behind.

I encountered this error when trying to install CytoNorm from GitHub.

[liabuffa97]

A couple of days ago, I was able to install flowSpectrum from GitHub, but now I encounter the same error when attempting to install any package from it.

[DavidRach]

Hi @liabuffa97, my QC dashboard website is failing with a similar error, so I think it might have been a general update style error related to download requests. I will look into it on Tuesday and get back to you with a fix. Best- David