Failed to install

[joonlee3]

Hi,

I was trying to install 'IndepthPathway' package but failed. I am currently using R4.3.0. Here is what I've got during the installation step.

Downloading GitHub repo wangxlab/IndepthPathway@HEAD ── R CMD build ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── ✔ checking for file ‘/tmp/RtmpHa7yJQ/remotesa8a798fc98/wangxlab-IndepthPathway-c56e587/DESCRIPTION’ (732ms) ─ preparing ‘IndepthPathway’: ✔ checking DESCRIPTION meta-information ... Warning: preCalmatrix.Rd:10: unknown macro '\tKEGG' Warning: preCalmatrix.Rd:11: unknown macro '\tKEGG' ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ building ‘IndepthPathway_0.0.0.9000.tar.gz’

Installing package into ‘/cloud-home/I0180769/R/x86_64-pc-linux-gnu-library/4.3.0’ (as ‘lib’ is unspecified)

• installing source package ‘IndepthPathway’ ... using staged installation R data * moving datasets to lazyload DB byte-compile and prepare package for lazy loading * help Warning: preCalmatrix.Rd:10: unknown macro '\tKEGG' Warning: preCalmatrix.Rd:11: unknown macro '\tKEGG' installing help indices building package indices testing if installed package can be loaded from temporary location Warning: S3 method ‘merge.pathway’ was declared in NAMESPACE but not found Error: package or namespace load failed for ‘IndepthPathway’ in namespaceExport(ns, exports): undefined exports: deambiguation.CSEA, deambiguation.GSEA Error: loading failed Execution halted

Any suggestions? Thanks.

Best, Joon

[hakobyansiras]

I have the same issue while installing the package. R version 4.2.3.

[pedriniedoardo]

same error with R4.2.1

[sanghoonleepitt]

@joonlee3, @hakobyansiras, @pedriniedoardo, thank you for your interest in IndepthPathway. We haven't tested the package in R ver. 4.3.0 yet and we found a couple of bugs on our end. We are testing it in R 4.3.0 and fixing the bugs. We will try to update you in a couple of days. Sorry for the inconvenience.

[sanghoonleepitt]

Thank you for your patience! I fixed all bugs and tested the package in R 4.3.0. Could you try to install the package and run the code again? The example input files are stored at /ExampleInputFile/ Please let us know if it doesn't work or if you find any bugs.

[pedriniedoardo]

Hello, thank you for fixing it! I can confirm the installation works fine now. Also, the vignette runs smoothly with this configuration:

> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /home/pedrini.edoardo/miniconda3/envs/env_R4.2_renv/lib/libopenblasp-r0.3.21.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] IndepthPathway_0.0.0.9000

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.10         pillar_1.9.0        compiler_4.2.1      BiocManager_1.30.21 RColorBrewer_1.1-3 
 [6] plyr_1.8.8          iterators_1.0.14    tools_4.2.1         nlme_3.1-162        lattice_0.21-8     
[11] lifecycle_1.0.3     tibble_3.2.1        gtable_0.3.3        mgcv_1.8-42         pkgconfig_2.0.3    
[16] rlang_1.1.1         igraph_1.4.3        foreach_1.5.2       Matrix_1.5-4.1      cli_3.6.1          
[21] rstudioapi_0.14     parallel_4.2.1      cluster_2.1.4       dplyr_1.1.2         stringr_1.5.0      
[26] generics_0.1.3      vctrs_0.6.2         grid_4.2.1          tidyselect_1.2.0    qvalue_2.30.0      
[31] glue_1.6.2          R6_2.5.1            fansi_1.0.4         influential_2.2.7   pheatmap_1.0.12    
[36] limma_3.54.2        ggplot2_3.4.2       reshape2_1.4.4      magrittr_2.0.3      codetools_0.2-19   
[41] MASS_7.3-60         scales_1.2.1        splines_4.2.1       permute_0.9-7       colorspace_2.1-0   
[46] renv_0.15.5         utf8_1.2.3          stringi_1.7.12      otuSummary_0.1.1    munsell_0.5.0      
[51] vegan_2.6-4        

[sanghoonleepitt]

@pedriniedoardo, thank you for your testing! While running IndepthPathway, if you have any questions, please let me know. I will try to help you more.