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bvieth / powsimR

Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.
https://bvieth.github.io/powsimR/
Artistic License 2.0
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error building vignette #51

Closed avrilcoghlan closed 3 years ago

avrilcoghlan commented 3 years ago

Hello, I get some error messages when trying to install powsimR. I was able to build it in the end, but only when I left out the bit about build_vignettes=TRUE. When I had included build_vignettes=TRUE I got an error message that said: E creating vignettes (lm 0.9s) --- re-building 'powsimR.Rmd' using rmarkdown Warning in engine$weave(file, quiet=quiet, enconding=enc): Pandoc (>=1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown vi. Quitting from lines 24-36 (powsimR.rmd) Error: processing vignette 'powsimR.Rmd' failed with diagonostics: there is no package called 'rmdformats' --- failed re-building 'powsimR.Rmd' SUMMARY: processing the following file failed: 'powsimR.Rmd' Error: Vignette re-building failed. Execution halted. Error: Failed to install 'powsimR' from GitHub.

Here is my sessionInfo:

R version 4.0.2 (2020-06-22) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C LC_TIME=English_United Kingdom.1252

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

other attached packages: [1] powsimR_1.2.3 gamlss.dist_5.1-7 MASS_7.3-51.6 devtools_2.3.1 usethis_1.6.1

loaded via a namespace (and not attached): [1] mixtools_1.2.0 softImpute_1.4 minpack.lm_1.2-1 lattice_0.20-41 haven_2.3.1 vctrs_0.3.4 fastICA_1.2-2
[8] mgcv_1.8-31 penalized_0.9-51 blob_1.2.1 survival_3.1-12 Rmagic_2.0.3 later_1.1.0.1 nloptr_1.2.2.2
[15] DBI_1.1.0 R.utils_2.10.1 SingleCellExperiment_1.10.1 rappdirs_0.3.1 Linnorm_2.12.0 dqrng_0.2.1 jpeg_0.1-8.1
[22] zlibbioc_1.34.0 MatrixModels_0.4-1 htmlwidgets_1.5.1 mvtnorm_1.1-1 future_1.18.0 UpSetR_1.4.0 parallel_4.0.2
[29] scater_1.16.2 irlba_2.3.3 DEoptimR_1.0-8 Rcpp_1.0.5 KernSmooth_2.23-17 DT_0.15 promises_1.1.1
[36] gdata_2.18.0 DDRTree_0.1.5 DelayedArray_0.14.1 limma_3.44.3 vegan_2.5-6 pkgload_1.1.0 Hmisc_4.4-1
[43] ShortRead_1.46.0 apcluster_1.4.8 RSpectra_0.16-0 fs_1.5.0 msir_1.3.2 mnormt_2.0.2 digest_0.6.25
[50] png_0.1-7 qlcMatrix_0.9.7 sctransform_0.2.1 cowplot_1.1.0 pkgconfig_2.0.3 docopt_0.7.1 DelayedMatrixStats_1.10.1
[57] ggbeeswarm_0.6.0 iterators_1.0.12 minqa_1.2.4 lavaan_0.6-7 reticulate_1.16 SummarizedExperiment_1.18.2 spam_2.5-1
[64] beeswarm_0.2.3 modeltools_0.2-23 xfun_0.17 zoo_1.8-8 tidyselect_1.1.0 ZIM_1.1.0 reshape2_1.4.4
[71] purrr_0.3.4 kernlab_0.9-29 EDASeq_2.22.0 viridisLite_0.3.0 snow_0.4-3 rtracklayer_1.48.0 pkgbuild_1.1.0
[78] rlang_0.4.7 hexbin_1.28.1 glue_1.4.2 RColorBrewer_1.1-2 fpc_2.2-7 matrixStats_0.56.0 stringr_1.4.0
[85] fields_11.4 ggsignif_0.6.0 DESeq2_1.28.1 SparseM_1.78 httpuv_1.5.4 class_7.3-17 BPSC_0.99.2
[92] BiocNeighbors_1.6.0 annotate_1.66.0 jsonlite_1.7.1 XVector_0.28.0 tmvnsim_1.0-2 bit_4.0.4 mime_0.9
[99] gridExtra_2.3 gplots_3.0.4 Rsamtools_2.4.0 zingeR_0.1.0 stringi_1.5.3 gmodels_2.18.1 processx_3.4.4
[106] bitops_1.0-6 cli_2.0.2 maps_3.3.0 RSQLite_2.2.0 tidyr_1.1.2 pheatmap_1.0.12 data.table_1.13.0
[113] rstudioapi_0.11 GenomicAlignments_1.24.0 nlme_3.1-148 qvalue_2.20.0 scran_1.16.0 fastcluster_1.1.25 locfit_1.5-9.4
[120] scone_1.12.0 listenv_0.8.0 cobs_1.3-4 R.oo_1.24.0 prabclus_2.3-2 segmented_1.2-0 dbplyr_1.4.4
[127] BiocGenerics_0.34.0 sessioninfo_1.1.1 readxl_1.3.1 lifecycle_0.2.0 ROTS_1.16.0 munsell_0.5.0 cellranger_1.1.0
[134] R.methodsS3_1.8.1 moments_0.14 hwriter_1.3.2 caTools_1.18.0 codetools_0.2-16 coda_0.19-3 Biobase_2.48.0
[141] GenomeInfoDb_1.24.2 vipor_0.4.5 htmlTable_2.0.1 bayNorm_1.6.0 rARPACK_0.11-0 xtable_1.8-4 SAVER_1.1.2
[148] ROCR_1.0-11 diptest_0.75-7 BiocManager_1.30.10 lpsymphony_1.16.0 abind_1.4-5 FNN_1.1.3 RANN_2.6.1
[155] askpass_1.1 sparsesvd_0.2 CompQuadForm_1.4.3 GenomicRanges_1.40.0 tibble_3.0.3 ggdendro_0.1.22 cluster_2.1.0
[162] future.apply_1.6.0 Matrix_1.2-18 ellipsis_0.3.1 prettyunits_1.1.1 shinyBS_0.61 NOISeq_2.31.0 shinydashboard_0.7.1
[169] mclust_5.4.6 igraph_1.2.5 ggstance_0.3.4 remotes_2.2.0 slam_0.1-47 testthat_2.3.2 doSNOW_1.0.18
[176] htmltools_0.5.0 BiocFileCache_1.12.1 GenomicFeatures_1.40.1 XML_3.99-0.5 ggpubr_0.4.0 DrImpute_1.0 foreign_0.8-80
[183] withr_2.2.0 fitdistrplus_1.1-1 BiocParallel_1.22.0 aroma.light_3.18.0 bit64_4.0.5 foreach_1.5.0 robustbase_0.93-6
[190] outliers_0.14 Biostrings_2.56.0 combinat_0.0-8 rsvd_1.0.3 iCOBRA_1.16.0 memoise_1.1.0 VGAM_1.1-3
[197] nonnest2_0.5-5 forcats_0.5.0 rio_0.5.16 geneplotter_1.66.0 permute_0.9-5 callr_3.4.4 ps_1.3.4
[204] curl_4.3 fdrtool_1.2.15 fansi_0.4.1 conquer_1.0.2 edgeR_3.30.3 checkmate_2.0.0 desc_1.2.0
[211] truncnorm_1.0-8 tensorA_0.36.1 DECENT_1.1.0 ellipse_0.4.2 ggplot2_3.3.2 openxlsx_4.1.5 rstatix_0.6.0
[218] ggrepel_0.8.2 scDD_1.12.0 rprojroot_1.3-2 tools_4.0.2 sandwich_2.5-1 magrittr_1.5 RCurl_1.98-1.2
[225] car_3.0-9 pbivnorm_0.6.0 bayesm_3.1-4 EBSeq_1.28.0 httr_1.4.2 assertthat_0.2.1 Rhdf5lib_1.10.1
[232] boot_1.3-25 globals_0.12.5 R6_2.4.1 nnet_7.3-14 progress_1.2.2 genefilter_1.70.0 gtools_3.8.2
[239] statmod_1.4.34 BiocSingular_1.4.0 rhdf5_2.32.2 splines_4.0.2 carData_3.0-4 colorspace_1.4-1 amap_0.8-18
[246] generics_0.0.2 stats4_4.0.2 NBPSeq_0.3.0 compositions_2.0-0 base64enc_0.1-3 baySeq_2.22.0 pillar_1.4.6
[253] HSMMSingleCell_1.8.0 GenomeInfoDbData_1.2.3 plyr_1.8.6 dotCall64_1.0-0 gtable_0.3.0 zip_2.1.1 SCnorm_1.10.0
[260] monocle_2.16.0 knitr_1.29 RcppArmadillo_0.9.900.3.0 latticeExtra_0.6-29 biomaRt_2.44.1 IRanges_2.22.2 fastmap_1.0.1
[267] doParallel_1.0.15 pscl_1.5.5 flexmix_2.3-15 quantreg_5.67 AnnotationDbi_1.50.3 broom_0.7.0 openssl_1.4.2
[274] scales_1.1.1 arm_1.11-2 backports_1.1.9 plotrix_3.7-8 IHW_1.16.0 S4Vectors_0.26.1 densityClust_0.3
[281] lme4_1.1-23 hms_0.5.3 DESeq_1.39.0 Rtsne_0.15 dplyr_1.0.2 shiny_1.5.0 grid_4.0.2
[288] Formula_1.2-3 blockmodeling_1.0.0 crayon_1.3.4 MAST_1.14.0 RUVSeq_1.22.0 viridis_0.5.1 rpart_4.1-15
[295] zinbwave_1.10.0 compiler_4.0.2

bvieth commented 3 years ago

Dear Avril,

thank you for your interest in powsimR! I am sorry to hear that you have encountered this issue.

Given your detailed error message, it appears that you are missing the R package rmdformats which is necessary to build the vignette. Given that it is not absolutely necessary to build it (you can also find it here) and the rmdformats package is only needed for this sole purpose, I have listed it under the Suggests in the DESCRIPTION file. This has the disadvantage that its installation is not checked and thus not automatically installed when it is missing in your R libraries. So, if you install rmdformats prior to powsimR the error should be resolved.

I will now include it in the manual installation guide as well.

As a side note, I have not tested powsimR on a Windows machine and it is therefore possible that a number of implemented methods using parallel computing when you specify NCores, might not work.

Kind regards Beate