error in loadCMapZscores #10
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Hello there! Could you please detail run 'sessionInfo()' so I know more details about your R session? Thank you!
… On 15 Apr 2020, at 22:48, KC ***@***.***> wrote:
Hi I was going through the tutorial and ran into this error:
zscores <- loadCMapZscores(perts[ , 1:10])
Loading data from /home/shared/Misc_studies/CMap_DepMap/cmapZscores.gctx...
Error in .local(.Object, ...) : unused argument (verbose = verbose)
Pls advise. Thank you.
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R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS
Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.so
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 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
LC_ADDRESS=C LC_TELEPHONE=C
LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils
datasets methods base
other attached packages:
[1] cmapR_0.99.19 pool_0.1.4.3
RPostgreSQL_0.6-2 DBI_1.1.0 stringr_1.4.0
dplyr_0.8.5
[7] tidyr_1.0.2 drugbankR_1.5 cTRAP_1.4
org.Hs.eg.db_3.10.0 AnnotationDbi_1.48.0
signatureSearch_1.0.4
[13] Rcpp_1.0.4.6 HDF5Array_1.14.3
SummarizedExperiment_1.16.1 DelayedArray_0.12.3
BiocParallel_1.20.1 matrixStats_0.56.0
[19] Biobase_2.46.0 GenomicRanges_1.38.0
GenomeInfoDb_1.22.1 IRanges_2.20.2
S4Vectors_0.24.4 signatureSearchData_1.0.0
[25] rhdf5_2.30.1 ExperimentHub_1.12.0
AnnotationHub_2.18.0 BiocFileCache_1.10.2 dbplyr_1.4.2
BiocGenerics_0.32.0
loaded via a namespace (and not attached):
[1] readxl_1.3.1 fastmatch_1.1-0
plyr_1.8.6 igraph_1.2.5
GSEABase_1.48.0
[6] splines_3.6.3 ggplot2_3.3.0
urltools_1.7.3 digest_0.6.25
htmltools_0.4.0
[11] GOSemSim_2.12.1 viridis_0.5.1
GO.db_3.10.0 fansi_0.4.1
magrittr_1.5
[16] memoise_1.1.0 prada_1.62.0
limma_3.42.2 readr_1.3.1
annotate_1.64.0
[21] graphlayouts_0.6.0 R.utils_2.9.2
askpass_1.1 enrichplot_1.6.1
prettyunits_1.1.1
[26] colorspace_1.4-1 rrcov_1.5-2
blob_1.2.1 rappdirs_0.3.1
ggrepel_0.8.2
[31] crayon_1.3.4 RCurl_1.98-1.1
jsonlite_1.6.1 graph_1.64.0 glue_1.4.0
[36] polyclip_1.10-0 gtable_0.3.0
zlibbioc_1.32.0 XVector_0.26.0
Rhdf5lib_1.8.0
[41] DEoptimR_1.0-8 scales_1.1.0
DOSE_3.12.0 mvtnorm_1.1-0
viridisLite_0.3.0
[46] xtable_1.8-4 progress_1.2.2
gridGraphics_0.5-0 bit_1.1-15.2
europepmc_0.3
[51] preprocessCore_1.48.0 htmlwidgets_1.5.1
httr_1.4.1 fgsea_1.12.0
RColorBrewer_1.1-2
[56] ellipsis_0.3.0 pkgconfig_2.0.3
XML_3.99-0.3 R.methodsS3_1.8.0
farver_2.0.3
[61] ggplotify_0.0.5 tidyselect_1.0.0
rlang_0.4.5 reshape2_1.4.4
later_1.0.0
[66] cellranger_1.1.0 munsell_0.5.0
BiocVersion_3.10.1 tools_3.6.3
visNetwork_2.0.9
[71] cli_2.0.2 RSQLite_2.2.0
ggridges_0.5.2 fastmap_1.0.1 yaml_2.2.1
[76] bit64_0.9-7 tidygraph_1.1.2
robustbase_0.93-6 purrr_0.3.3
ggraph_2.0.2
[81] pbapply_1.4-2 mime_0.9
R.oo_1.23.0 DO.db_2.9 xml2_1.3.1
[86] biomaRt_2.42.1 compiler_3.6.3
rstudioapi_0.11 curl_4.3
interactiveDisplayBase_1.24.0
[91] affyio_1.56.0 tibble_3.0.0
tweenr_1.0.1 pcaPP_1.9-73
stringi_1.4.6
[96] lattice_0.20-41 Matrix_1.2-18
vctrs_0.2.4 pillar_1.4.3
lifecycle_0.2.0
[101] BiocManager_1.30.10 triebeard_0.3.0
data.table_1.12.8 cowplot_1.0.0
bitops_1.0-6
[106] httpuv_1.5.2 qvalue_2.18.0
R6_2.4.1 affy_1.64.0
promises_1.1.0
[111] gridExtra_2.3 MASS_7.3-51.5
assertthat_0.2.1 openssl_1.4.1
GenomeInfoDbData_1.2.2
[116] hms_0.5.3 clusterProfiler_3.14.3
grid_3.6.3 rvcheck_0.1.8
ggforce_0.3.1
[121] shiny_1.4.0.2
On Wed, Apr 15, 2020 at 7:00 PM Nuno Agostinho <notifications@github.com>
wrote:
… Hello there! Could you please detail run 'sessionInfo()' so I know more
details about your R session? Thank you!
> On 15 Apr 2020, at 22:48, KC ***@***.***> wrote:
>
>
> Hi I was going through the tutorial and ran into this error:
>
> zscores <- loadCMapZscores(perts[ , 1:10])
> Loading data from
/home/shared/Misc_studies/CMap_DepMap/cmapZscores.gctx...
> Error in .local(.Object, ...) : unused argument (verbose = verbose)
>
> Pls advise. Thank you.
>
> —
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub, or unsubscribe.
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ghost
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Hey @kengcher, why did you close this thread? Is your issue already resolved? |
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Hi I was going through the tutorial and ran into this error:
zscores <- loadCMapZscores(perts[ , 1:10])
Loading data from /home/shared/Misc_studies/CMap_DepMap/cmapZscores.gctx...
Error in .local(.Object, ...) : unused argument (verbose = verbose)
Pls advise. Thank you.
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