Error gseGO in multicore mclapply

[StephaneKazmierczak]

in R3.3 I was getting in the multicore mode with mclapply, for all core except one the following error:
Rcpp::exception in rsqlite_send_query(conn@ptr, statement): database disk image is malformed

After updating to R3.4.3 single core and multi core are now getting
<simpleError in registered()[[bpparamClass]]: attempt to select less than one element in get1index>
in addition to
<Rcpp::exception in rsqlite_send_query(conn@ptr, statement): database disk image is malformed>

[StephaneKazmierczak]

I updated all packages making sure everything is up to date now I am getting a different error while trying the demo example:

gseGO(geneList     = geneList,
            OrgDb        = org.Hs.eg.db,
            ont          = "CC",
            nPerm        = 1000,
            minGSSize    = 100,
            maxGSSize    = 500,
            pvalueCutoff = 0.05,
            verbose      = T)

preparing geneSet collections...
GSEA analysis...
Error in data.frame(ID = as.character(tmp_res$pathway), Description = Description,  : 
  row names contain missing values

R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.7.0
LAPACK: /usr/lib/lapack/liblapack.so.3.7.0

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

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

other attached packages:
[1] org.Hs.eg.db_3.5.0 AnnotationDbi_1.40.0 IRanges_2.12.0 S4Vectors_0.16.0 Biobase_2.38.0 BiocGenerics_0.24.0 clusterProfiler_3.6.0
[8] DOSE_3.4.0 cmapR_1.0 data.table_1.10.4-3 rhdf5_2.22.0 dplyr_0.7.4 readr_1.1.1 BiocInstaller_1.28.0

loaded via a namespace (and not attached):
[1] qvalue_2.10.0 fgsea_1.4.0 reshape2_1.4.3 purrr_0.2.4 splines_3.4.3 colorspace_1.3-2 blob_1.1.0
[8] rlang_0.1.6 pillar_1.0.1 glue_1.2.0 DBI_0.7 BiocParallel_1.12.0 bit64_0.9-7 bindrcpp_0.2
[15] rvcheck_0.0.9 plyr_1.8.4 bindr_0.1 stringr_1.2.0 zlibbioc_1.24.0 munsell_0.4.3 GOSemSim_2.4.0
[22] gtable_0.2.0 memoise_1.1.0 labeling_0.3 Rcpp_0.12.14 scales_0.5.0 DO.db_2.9 bit_1.1-12
[29] gridExtra_2.3 fastmatch_1.1-0 ggplot2_2.2.1 hms_0.4.0 digest_0.6.13 stringi_1.1.6 grid_3.4.3
[36] tools_3.4.3 magrittr_1.5 lazyeval_0.2.1 tibble_1.4.1 RSQLite_2.0 GO.db_3.5.0 tidyr_0.7.2
[43] pkgconfig_2.0.1 assertthat_0.2.0 R6_2.2.2 igraph_1.1.2 compiler_3.4.3

[GuangchuangYu]

any reproducible example?

[StephaneKazmierczak]

Yes I am getting the same error in single core now as well:
data(geneList, package="DOSE")
gsego <- gseGO(geneList = geneList,
OrgDb = org.Hs.eg.db,
ont = "CC",
nPerm = 1000,
minGSSize = 100,
maxGSSize = 500,
pvalueCutoff = 0.05,
verbose = T)

[GuangchuangYu]

can't reproduce your issue.

[StephaneKazmierczak]

Hi thank you for the reply, something must be wrong with my R server configuration then, could you please provide your R session details?

[GuangchuangYu]

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.2

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] clusterProfiler_3.6.0 DOSE_3.4.0            rvcheck_0.0.9
[4] rmarkdown_1.8         roxygen2_6.0.1        magrittr_1.5
[7] BiocInstaller_1.28.0

loaded via a namespace (and not attached):
 [1] qvalue_2.10.0        fgsea_1.4.0          reshape2_1.4.3
 [4] purrr_0.2.4          splines_3.4.3        colorspace_1.3-2
 [7] htmltools_0.3.6      stats4_3.4.3         blob_1.1.0
[10] rlang_0.1.6          withr_2.1.1          glue_1.2.0
[13] DBI_0.7              BiocParallel_1.12.0  BiocGenerics_0.24.0
[16] bit64_0.9-7          plyr_1.8.4           stringr_1.2.0
[19] munsell_0.4.3        GOSemSim_2.4.0       commonmark_1.4
[22] gtable_0.2.0         devtools_1.13.4      memoise_1.1.0
[25] evaluate_0.10.1      Biobase_2.38.0       knitr_1.18
[28] IRanges_2.12.0       parallel_3.4.3       AnnotationDbi_1.40.0
[31] Rcpp_0.12.14         backports_1.1.2      scales_0.5.0
[34] DO.db_2.9            S4Vectors_0.16.0     bit_1.1-12
[37] gridExtra_2.3        fastmatch_1.1-0      ggplot2_2.2.1
[40] digest_0.6.13        stringi_1.1.6        rprojroot_1.3-2
[43] grid_3.4.3           tools_3.4.3          lazyeval_0.2.1
[46] tibble_1.3.4         RSQLite_2.0          GO.db_3.5.0
[49] tidyr_0.7.2          pkgconfig_2.0.1      data.table_1.10.4-3
[52] xml2_1.1.1           rstudioapi_0.7       R6_2.2.2
[55] igraph_1.1.2         compiler_3.4.3

[StephaneKazmierczak]

Thank you so much, most of my packages are the same or a little bit more recent. I found that from an R console session (ssh to my server) this snippet work, however, it fails from the web session (R studio server) with the same server and exact same import/package version...

[straightnochaser]

Sorry for bringing up an old issue.

@StephaneKazmierczak I think I know what the problem is (had it an solved it this morning). Have you tried preload the org.Hs.eg.db prior to using mclapply? Alternatively, is it loading other required packages at the time of running mclapply?