Error: processing vignette 'psuper_intro.Rmd' failed with diagnostics: E> argument "exclude" is missing, with no default
qrzhang opened this issue · 5 comments
qrzhang commented
Hi psupertime team,
psupertime is truly a great package that I'm looking for. But I failed to install it on my machine with both R 3.6.2 and R 4.0.0. The error message is as following.
─ installing the package to build vignettes
E creating vignettes (23.6s)
--- re-building ‘psuper_intro.Rmd’ using rmarkdown
Warning: package 'S4Vectors' was built under R version 3.6.3
Warning: package 'GenomeInfoDb' was built under R version 3.6.3
Warning: package 'DelayedArray' was built under R version 3.6.3
Quitting from lines 37-50 (psuper_intro.Rmd)
Error: processing vignette 'psuper_intro.Rmd' failed with diagnostics:
argument "exclude" is missing, with no default
--- failed re-building ‘psuper_intro.Rmd’
SUMMARY: processing the following file failed:
‘psuper_intro.Rmd’
Error: Vignette re-building failed.
Execution halted
Error: Failed to install 'psupertime' from GitHub:
System command 'R' failed, exit status: 1, stdout + stderr (last 10 lines):
E> Quitting from lines 37-50 (psuper_intro.Rmd)
E> Error: processing vignette 'psuper_intro.Rmd' failed with diagnostics:
E> argument "exclude" is missing, with no default
E> --- failed re-building ‘psuper_intro.Rmd’
E>
E> SUMMARY: processing the following file failed:
E> ‘psuper_intro.Rmd’
E>
E> Error: Vignette re-building failed.
E> Execution haltedEven though I can successfully install this package without building vignettes devtools::install_github('wmacnair/psupertime', build_vignettes=FALSE) Then I follow the vignette, the same error occurs at command psuper_obj = psupertime(acinar_hvg_sce, y, sel_genes='all')
> sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.5
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] SingleCellExperiment_1.8.0 SummarizedExperiment_1.16.1 DelayedArray_0.12.3 BiocParallel_1.20.1 matrixStats_0.56.0
[6] Biobase_2.46.0 GenomicRanges_1.38.0 GenomeInfoDb_1.22.1 IRanges_2.20.2 S4Vectors_0.24.4
[11] BiocGenerics_0.32.0 psupertime_0.2.6 glmnet_4.0 Matrix_1.2-18
loaded via a namespace (and not attached):
[1] bitops_1.0-6 fs_1.4.1 usethis_1.6.1 bit64_0.9-7 devtools_2.3.0
[6] RColorBrewer_1.1-2 rprojroot_1.3-2 tools_3.6.2 backports_1.1.7 R6_2.4.1
[11] irlba_2.3.3 vipor_0.4.5 DBI_1.1.0 colorspace_1.4-1 withr_2.2.0
[16] gridExtra_2.3 prettyunits_1.1.1 processx_3.4.2 bit_1.1-15.2 curl_4.3
[21] compiler_3.6.2 graph_1.64.0 cli_2.0.2 BiocNeighbors_1.4.2 SparseM_1.78
[26] desc_1.2.0 topGO_2.38.1 scales_1.1.1 callr_3.4.3 stringr_1.4.0
[31] digest_0.6.25 XVector_0.26.0 scater_1.14.6 pkgconfig_2.0.3 sessioninfo_1.1.1
[36] limma_3.42.2 rlang_0.4.6 RSQLite_2.2.0 rstudioapi_0.11 DelayedMatrixStats_1.8.0
[41] shape_1.4.4 RCurl_1.98-1.2 magrittr_1.5 BiocSingular_1.2.2 GO.db_3.10.0
[46] GenomeInfoDbData_1.2.2 Rcpp_1.0.4 ggbeeswarm_0.6.0 munsell_0.5.0 fansi_0.4.1
[51] viridis_0.5.1 lifecycle_0.2.0 stringi_1.4.6 edgeR_3.28.1 zlibbioc_1.32.0
[56] pkgbuild_1.0.8 blob_1.2.1 grid_3.6.2 dqrng_0.2.1 forcats_0.5.0
[61] crayon_1.3.4 lattice_0.20-38 cowplot_1.0.0 locfit_1.5-9.4 knitr_1.28
[66] ps_1.3.3 pillar_1.4.4 igraph_1.2.5 fastcluster_1.1.25 codetools_0.2-16
[71] pkgload_1.1.0 glue_1.4.1 scran_1.14.6 data.table_1.12.8 remotes_2.1.1
[76] vctrs_0.3.0 foreach_1.5.0 testthat_2.3.2 gtable_0.3.0 assertthat_0.2.1
[81] ggplot2_3.3.1 xfun_0.14 rsvd_1.0.3 viridisLite_0.3.0 tibble_3.0.1
[86] iterators_1.0.12 AnnotationDbi_1.48.0 beeswarm_0.2.3 memoise_1.1.0 statmod_1.4.34 Will appreciate any reply!
vtosevski commented
Dear Will,
Indeed there seems to be a problem now that wasn't there before. I really like psupertime concept and use your package quite often. I went to re-run some previous code now and got the same error message when running main psupertime function:
Error in glmnet(glmnet.data$x, glmnet.data$y, family = "binomial", weights = glmnet.data$weights, :
argument "exclude" is missing, with no default
This wasn't there last time I ran it (I am guessing sometime in March). I (naively) thought the recent update to glmnet package might be causing it and tried the older versions of it, but that didn't help.
Any suggestion how to overcome this problem?
Thanks,
Vinko
> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=de_CH.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=de_CH.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=de_CH.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=de_CH.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] psupertime_0.2.6 topGO_2.38.1 SparseM_1.78 GO.db_3.10.0 AnnotationDbi_1.48.0
[6] IRanges_2.20.2 S4Vectors_0.24.4 Biobase_2.46.0 graph_1.64.0 BiocGenerics_0.32.0
[11] fastcluster_1.1.25 harmony_1.0 Rcpp_1.0.4.6 qs_0.22.1 patchwork_1.0.0
[16] ggplot2_3.3.1 dplyr_1.0.0 Matrix_1.2-18 Seurat_3.1.5
loaded via a namespace (and not attached):
[1] plyr_1.8.6 igraph_1.2.5 lazyeval_0.2.2
[4] splines_3.6.3 RApiSerialize_0.1.0 BiocParallel_1.20.1
[7] listenv_0.8.0 GenomeInfoDb_1.22.1 scater_1.14.6
[10] digest_0.6.25 foreach_1.5.0 htmltools_0.4.0
[13] viridis_0.5.1 magrittr_1.5 memoise_1.1.0
[16] cluster_2.1.0 ROCR_1.0-11 limma_3.42.2
[19] globals_0.12.5 matrixStats_0.56.0 colorspace_1.4-1
[22] blob_1.2.1 rappdirs_0.3.1 ggrepel_0.8.2
[25] xfun_0.14 crayon_1.3.4 RCurl_1.98-1.2
[28] jsonlite_1.6.1 stringfish_0.12.1 survival_3.1-12
[31] zoo_1.8-8 iterators_1.0.12 ape_5.4
[34] glue_1.4.1 gtable_0.3.0 zlibbioc_1.32.0
[37] XVector_0.26.0 leiden_0.3.3 DelayedArray_0.12.3
[40] BiocSingular_1.2.2 future.apply_1.5.0 shape_1.4.4
[43] SingleCellExperiment_1.8.0 scales_1.1.1 DBI_1.1.0
[46] edgeR_3.28.1 viridisLite_0.3.0 reticulate_1.16
[49] dqrng_0.2.1 bit_1.1-15.2 rsvd_1.0.3
[52] tsne_0.1-3 glmnet_2.0-16 htmlwidgets_1.5.1
[55] httr_1.4.1 RColorBrewer_1.1-2 ellipsis_0.3.1
[58] ica_1.0-2 pkgconfig_2.0.3 uwot_0.1.8
[61] locfit_1.5-9.4 tidyselect_1.1.0 rlang_0.4.6
[64] reshape2_1.4.4 munsell_0.5.0 tools_3.6.3
[67] generics_0.0.2 RSQLite_2.2.0 ggridges_0.5.2
[70] stringr_1.4.0 knitr_1.28 bit64_0.9-7
[73] fitdistrplus_1.1-1 purrr_0.3.4 RANN_2.6.1
[76] pbapply_1.4-2 future_1.17.0 nlme_3.1-148
[79] scran_1.14.6 compiler_3.6.3 rstudioapi_0.11
[82] beeswarm_0.2.3 plotly_4.9.2.1 png_0.1-7
[85] tibble_3.0.1 statmod_1.4.34 stringi_1.4.6
[88] forcats_0.5.0 lattice_0.20-41 vctrs_0.3.1
[91] pillar_1.4.4 lifecycle_0.2.0 BiocManager_1.30.10
[94] lmtest_0.9-37 RcppAnnoy_0.0.16 BiocNeighbors_1.4.2
[97] data.table_1.12.8 cowplot_1.0.0 bitops_1.0-6
[100] irlba_2.3.3 GenomicRanges_1.38.0 R6_2.4.1
[103] KernSmooth_2.23-17 gridExtra_2.3 vipor_0.4.5
[106] codetools_0.2-16 MASS_7.3-51.6 SummarizedExperiment_1.16.1
[109] withr_2.2.0 sctransform_0.2.1 GenomeInfoDbData_1.2.2
[112] grid_3.6.3 tidyr_1.1.0 DelayedMatrixStats_1.8.0
[115] Rtsne_0.15 tinytex_0.23 ggbeeswarm_0.6.0
wmacnair commented
Hi both, thanks for pointing this out, and for the detailed bug reports. I'll have a look tomorrow - hopefully it's an easy fix!
Cheers, Will
wmacnair commented
Hi @qrzhang @vtosevski, I've hopefully fixed the bug - please check and I'll reopen if there's still a problem :)
Will
vtosevski commented
Hi @wmacnair
Yes, all is good now, both the installation with vignette building and also the running of the main psupertime function. Perhaps, to stay ahead of the curve, you wish the consider the following warning message that I am getting when running psupertime_go_analysis function. Apparently, it will become an error message soon.
Warning messages:
1: In melt(x_data, varnames = c("cell_id", "symbol")) :
The melt generic in data.table has been passed a matrix and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is deprecated, and this redirection is now deprecated as well. To continue using melt methods from reshape2 while both libraries are attached, e.g. melt.list, you can prepend the namespace like reshape2::melt(x_data). In the next version, this warning will become an error.
2: In melt(x_data, varnames = c("cell_id", "symbol")) :
The melt generic in data.table has been passed a matrix and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is deprecated, and this redirection is now deprecated as well. To continue using melt methods from reshape2 while both libraries are attached, e.g. melt.list, you can prepend the namespace like reshape2::melt(x_data). In the next version, this warning will become an error.
Thank you so much for the swift response!
Vinko
wmacnair commented
Right, I have seen that error message in other contexts. Thanks, may tweak to fix it.
Cheers, Will