Failing to retrieve results for genes that produce results months back and from the example genes

[MikeKatz45]

Hello, I've recently had the need to re-run an analysis I did a few months ago and was surprised to see I couldn't reproduce the results. Upon trying with a minimal example (vignette example) I realized that the package is currently not able to retrieve any info from the database using the R wrapper. A co-worker also had this problem working in a different machine. I opened a bioconductor thread a few days ago with more details (post) but no one seemed to know what was going on.

[LBosshard]

Hello, can you install the latest version (1.16) from Bioconductor and retry: library(rDGIdb) genes <- c("TNF", "AP1", "AP2", "XYZA") result <- queryDGIdb(genes) resultSummary(result) Please let me know if the problem persists.

[MikeKatz45]

I uninstalled the package using remove.packages() and re-installed using the link provided. The problem persists, here is the sessionInfo() output.

`R version 4.0.3 (2020-10-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19041)

Matrix products: default

locale: [1] LC_COLLATE=Spanish_Mexico.1252 LC_CTYPE=Spanish_Mexico.1252
[3] LC_MONETARY=Spanish_Mexico.1252 LC_NUMERIC=C
[5] LC_TIME=Spanish_Mexico.1252

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

other attached packages: [1] rDGIdb_1.14.0

loaded via a namespace (and not attached): [1] httr_1.4.2 BiocManager_1.30.10 compiler_4.0.3
[4] R6_2.4.1 tools_4.0.3 curl_4.3
[7] jsonlite_1.6.1 `

The problem seems to be that BiocManager does not install 1.16 by default. It could also be a problem on my side, but I can't think of what. I also tried uninstalling and re-installing BiocManager and then re-installing rDGIdb, but version 1.14 keeps getting installed instead of 1.16.

[LBosshard]

Do you get an error message for the installation when you try: remove.packages("rDGIdb") .rs.restartR() BiocManager::install("rDGIdb",version = 3.12)

[MikeKatz45]

Yeah, I did get an error message. However this was the way to go to solve it as after the error message, another message said that I should do BiocManager::install(version = 3.12). Here is what I did:

remove.packages("rDGIdb")
.rs.restartR() # or manually restart R
 BiocManager::install(version = 3.12) # said yes to all prompts
BiocManager::install("rDGIdb",version = 3.12)

library(rDGIdb)
genes <- c("TNF", "AP1", "AP2", "XYZA")
result <- queryDGIdb(genes)
resultSummary(result)

Everything is working fine now, what happened here? Just an outdated BiocManager? It is a bit weird since I tried uninstalling and installing BiocManager before. I'd expect this to update BiocManager when re-installing but that did not happen.

[LBosshard]

I am glad that rDGIdb is working now. It is indeed weird that the update was not done automatically when re-installing. Maybe the package was still loaded in the r session. It cannot be updated while the package is loaded.

[wfma]

hey all i also had the same problem just now- updating biocmanager and then rdgidb seems to fix it!