singularity image not finding ggplot

[trum994]

Hi Nicolas,

I'm trying to run the singularity container (with the test data set) but coming across this error near the end:

My command looks something like this: time singularity exec hicpro_latest_ubuntu.img HiC-Pro -c /myPath/hicproRun/myRun1/myRun1_config.txt -i /myPath/hicproRun/myRun1/in -o /myPath/hicproRun/myRun1/out/

...
Sun Jun 21 21:59:37 PDT 2020
Merge stat files per sample ...
Logs: logs/dixon_2M/merge_stats.log
Logs: logs/dixon_2M_2/merge_stats.log

--------------------------------------------
Sun Jun 21 21:59:37 PDT 2020
Run quality checks for all samples ...
Logs: logs/dixon_2M/make_Rplots.log
make: *** [/usr/local/bin/HiC-Pro_2.11.4/bin/../scripts//Makefile:181: hic_qc] Error 1

Digging deeper I come across this in the logs file:

> ## Make plots
> mat_r1 <- getMapMat(stats_per_sample_r1[1], stats_per_sample_r1[2], stats_per_sample_r1[3], stats_per_sample_r1[4])
> mat_r1$lab <- factor(mat_r1$lab, levels=c("n.un","n.loc","n.glob","n.map"))
> p1 <- ploMapStat(mat_r1, sampleName=sampleName, tag="R1")
Loading required package: RColorBrewer
Loading required package: ggplot2
Error: package or namespace load failed for 'ggplot2' in rbind(info, getNamespaceInfo(env, "S3methods")):
 number of columns of matrices must match (see arg 2)
Loading required package: grid
Error in ggplot(mat, aes(x = p, as.numeric(count), fill = lab)) : 
  could not find function "ggplot"
Calls: ploMapStat
Execution halted

Happy to help further with debugging. Please let me know. Thank you!

[nservant]

Hi, Could you please try with this one ? https://zerkalo.curie.fr/partage/HiC-Pro/singularity_images/hicpro_3.0.0_ubuntu.img Thanks

[trum994]

Thanks for the quick response Nicolas.

I just ran it. Same thing I'm afraid:

make: *** [/usr/local/bin/HiC-Pro_3.0.0/bin/../scripts//Makefile:181: hic_qc] Error 1 In logs:

tail plot_mapping_portion.Rout
> p1 <- ploMapStat(mat_r1, sampleName=sampleName, tag="R1")
Loading required package: RColorBrewer
Loading required package: ggplot2
Error: package or namespace load failed for 'ggplot2' in rbind(info, getNamespaceInfo(env, "S3methods")):
 number of columns of matrices must match (see arg 2)
Loading required package: grid
Error in ggplot(mat, aes(x = p, as.numeric(count), fill = lab)) : 
  could not find function "ggplot"
Calls: ploMapStat
Execution halted

[trum994]

Update: By unsetting the environment variable $R_LIB (originally set in my .bashrc) I was able to workaround this issue. unset R_LIBS