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Comments (11)

lpantano avatar lpantano commented on June 12, 2024 1

hi @GrothmLab , can you try to install the version from main branch?

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gowgowuk avatar gowgowuk commented on June 12, 2024 1

I think I got it to work using:

devtools::install_github("lpantano/DEGreport")

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zellerivo avatar zellerivo commented on June 12, 2024

Hi Philippe,
you have asessed the problem absoulutely correct. As a workaround solution, try to source the clustering.R file and load the library(dendextend) manually. And probably you will also need library(tibble) and library(tidyr). Bug will be fixed soon, thanks for pointing it out

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gowgowuk avatar gowgowuk commented on June 12, 2024

Hello again,

I've tried to install the latest version you mentioned as temporary fix in issue #62 (avoid using dendextend). However, I have now another error:
Error in degPatterns(vst_data, time = "time", metadata = colData(dds_time), :
object 'skipDendrogram' not found

The version of the package I am using is now: DEGreport_1.39.4

Thanks

Philippe

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lpantano avatar lpantano commented on June 12, 2024

Hi, can you type in the console degPatterns and see if in the code you see, you can spot the parameter name? I am fixing the documentation in case that is the problem, but want to make sure the code has the right parameter name.

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lpantano avatar lpantano commented on June 12, 2024

Can you install again from the main branch, there was a typo. thanks

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gowgowuk avatar gowgowuk commented on June 12, 2024

Hello, it seems to work now. Thanks!

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GrothmLab avatar GrothmLab commented on June 12, 2024

Hi, has this issue been fixed already? I just got the same error. Thanks

> clusters_ntdC_all <- degPatterns(mat[1:100,], design, time="treatment",col="genotype", nClusters = 10)
Working with 100 genes.
Working with 54 genes after filtering: minc > 15
Joining with `by = join_by(merge)`
Joining with `by = join_by(merge)`
Error in set(., "labels", "") : could not find function "set"

> sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 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/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0

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       

time zone: Etc/UTC
tzcode source: system (glibc)

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] DEGreport_1.39.4            DESeq2_1.42.0               SummarizedExperiment_1.32.0 Biobase_2.62.0              MatrixGenerics_1.14.0      
 [6] matrixStats_1.2.0           GenomicRanges_1.54.1        GenomeInfoDb_1.38.6         IRanges_2.36.0              S4Vectors_0.40.2           
[11] BiocGenerics_0.48.1         biomaRt_2.58.2

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GrothmLab avatar GrothmLab commented on June 12, 2024

Now it works! Thanks!!

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danielsilvasilva avatar danielsilvasilva commented on June 12, 2024

hi @GrothmLab , can you try to install the version from main branch?

Could you please elaborate on how "install the version from main branch"?
I've tried

devtools::install_git("https://[email protected]/packages/DEGreport")

and got the following error:

Error: Failed to install 'unknown package' from Git:
  Command failed (1)
In addition: Warning messages:
1: In system(full, intern = TRUE, ignore.stderr = quiet) :
  running command ''/usr/bin/git' ls-remote https://[email protected]/packages/DEGreport  2>/dev/null' had status 1
2: In system(full, intern = TRUE, ignore.stderr = quiet) :
  running command ''/usr/bin/git' ls-remote https://[email protected]/packages/DEGreport  2>/dev/null' had status 1

Thank you very much!

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danielsilvasilva avatar danielsilvasilva commented on June 12, 2024

I think I got it to work using:

devtools::install_github("lpantano/DEGreport")

Thank you. It worked!

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