I am very new to R. Working mostly with Seurat package to evaluate my single-cell RNAseq data.
Today I wanted to update the R version and RStudio. After that I had problems using installed packages. This is my problem:
> install.packages("Seurat", dependencies = TRUE)
Installing package into ‘C:/Users/benne/AppData/Local/R/win-library/4.2’
(as ‘lib’ is unspecified)
Warning in install.packages :
dependencies ‘S4Vectors’, ‘SummarizedExperiment’, ‘SingleCellExperiment’, ‘MAST’, ‘DESeq2’, ‘BiocGenerics’, ‘GenomicRanges’, ‘GenomeInfoDb’, ‘IRanges’, ‘rtracklayer’, ‘monocle’, ‘Biobase’, ‘limma’ are not available
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/Seurat_4.2.0.zip'
Content type 'application/zip' length 2376157 bytes (2.3 MB)
downloaded 2.3 MB
package ‘Seurat’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\benne\AppData\Local\Temp\RtmpIlveV0\downloaded_packages
> library(Seurat)
Error: package or namespace load failed for ‘Seurat’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘spatstat.data’
I think, there is no problem with the installation of Seurat-package but I cannot make the library-function work. I found other topics that tried to solve that problem but they did not help me.
What could be the problem? With the old R/RStudio version everything worked well. After the update I had to install the RTools42 because it said I have to do that. I have never done that before, why today??
I really hope, you guys may help me. I am totally lost!!
Attached my sessionInfo():
> sessionInfo()
R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22000)
Matrix products: default
locale:
[1] LC_COLLATE=German_Germany.utf8 LC_CTYPE=German_Germany.utf8 LC_MONETARY=German_Germany.utf8
[4] LC_NUMERIC=C LC_TIME=German_Germany.utf8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] httr_1.4.4 tidyr_1.2.1 viridisLite_0.4.1 jsonlite_1.8.2 splines_4.2.1
[6] leiden_0.4.3 shiny_1.7.2 sp_1.5-0 ggrepel_0.9.1 globals_0.16.1
[11] pillar_1.8.1 lattice_0.20-45 glue_1.6.2 reticulate_1.26 digest_0.6.29
[16] RColorBrewer_1.1-3 promises_1.2.0.1 colorspace_2.0-3 plyr_1.8.7 cowplot_1.1.1
[21] htmltools_0.5.3 httpuv_1.6.6 Matrix_1.5-1 pkgconfig_2.0.3 listenv_0.8.0
[26] purrr_0.3.5 xtable_1.8-4 patchwork_1.1.2 scales_1.2.1 RANN_2.6.1
[31] later_1.3.0 Rtsne_0.16 spatstat.utils_2.3-1 tibble_3.1.8 generics_0.1.3
[36] ggplot2_3.3.6 ellipsis_0.3.2 ROCR_1.0-11 pbapply_1.5-0 SeuratObject_4.1.2
[41] lazyeval_0.2.2 cli_3.4.1 survival_3.3-1 magrittr_2.0.3 mime_0.12
[46] future_1.28.0 fansi_1.0.3 parallelly_1.32.1 MASS_7.3-57 ica_1.0-3
[51] progressr_0.11.0 tools_4.2.1 fitdistrplus_1.1-8 data.table_1.14.2 lifecycle_1.0.3
[56] matrixStats_0.62.0 stringr_1.4.1 plotly_4.10.0 munsell_0.5.0 cluster_2.1.3
[61] irlba_2.3.5.1 compiler_4.2.1 rlang_1.0.6 scattermore_0.8 grid_4.2.1
[66] ggridges_0.5.4 RcppAnnoy_0.0.19 htmlwidgets_1.5.4 igraph_1.3.5 miniUI_0.1.1.1
[71] gtable_0.3.1 codetools_0.2-18 reshape2_1.4.4 R6_2.5.1 gridExtra_2.3
[76] zoo_1.8-11 dplyr_1.0.10 fastmap_1.1.0 future.apply_1.9.1 rgeos_0.5-9
[81] utf8_1.2.2 KernSmooth_2.23-20 stringi_1.7.8 parallel_4.2.1 Rcpp_1.0.9
[86] sctransform_0.3.5 vctrs_0.4.2 png_0.1-7 tidyselect_1.2.0 lmtest_0.9-40
Thank you so much!
I tried to find out what the problem could be. I had hope that the installation of RTools42 may work but that does not make it better. The error still occurs.
Issue occurred for me as well after upgrading to R-4.2.1. Following steps helped me resolve the issue:
Restart the computer after successful installation of R Tools
Run following commands
install.packages('spatstat.data')
install.packages('spatstat.core')
After RTools wraps up it's compilation as mentioned in answer by Maso Sato
Library(Seurat) should load fine!
I had a similar problem with my installation of R, RStudio, and Seurat today (2022/10/26).
(I did not have a problem on another computer a few weeks ago).
install.packages('Seurat') said that I should install RTools.
I did so, and I got a similar error messages as yours when executing library(Seurat).
Then, I executed install.packages('spatstat.data').
RTools had to recompile various things (gcc), but at the end, library(Seurat) ran smoothly.
Related
I'm on Windows 10.
I want to send a command to a Terminal in RStudio using the rstudioapi. For example:
termId <- rstudioapi::terminalCreate()
rstudioapi::terminalSend(termId, 'dir\n')
My issue is that although the command is sent to the terminal, it does not run automatically. The cursor stays at the end of the line and I need to manually go to the terminal and press Enter.
I have seen many other terminal questions which have the \n at the end of the commands, so I'm certain it should work.
What am I doing wrong?
Thanks!
> sessionInfo()
R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)
Matrix products: default
locale:
[1] LC_COLLATE=Spanish_Argentina.utf8 LC_CTYPE=Spanish_Argentina.utf8 LC_MONETARY=Spanish_Argentina.utf8
[4] LC_NUMERIC=C LC_TIME=Spanish_Argentina.utf8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rstudioapi_0.13 RPostgres_1.4.4 DBI_1.1.3
loaded via a namespace (and not attached):
[1] bit_4.0.4 compiler_4.2.1 ellipsis_0.3.2 cli_3.3.0 hms_1.1.1 tools_4.2.1 Rcpp_1.0.8.3
[8] bit64_4.0.5 vctrs_0.4.1 blob_1.2.3 lifecycle_1.0.1 pkgconfig_2.0.3 rlang_1.0.3
In case somebody has the same issue:
I simply replaced the \n with \r and it worked. Don't really understand it as in another laptop it works fine with \n.
trying to follow the quanteda tutorial, I'm running into problems here with the programme; executing the following code, I get error messages hinting at problems with packages I cannot resolve.
> require(quanteda)
> require(quanteda.corpora)
> require(ggplot2)
> corp_tweets <- download(url = 'https://www.dropbox.com/s/846skn1i5elbnd2/data_corpus_sampletweets.rds?dl=1')
Error in loadNamespace(name) : there is no package called ‘digest’
As the package seems to be missing, I tried loading it and get:
> require("digest")
Loading required package: digest
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘digest’
Now, I try installing it - again, without success.
> install.packages("digest")
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/digest_0.6.20.zip'
Content type 'application/zip' length 223139 bytes (217 KB)
downloaded 217 KB
package ‘digest’ successfully unpacked and MD5 sums checked
Warning in install.packages :
cannot remove prior installation of package ‘digest’
The downloaded binary packages are in
C:\Users\my_username\AppData\Local\Temp\Rtmpaunnzu\downloaded_packages
Does anyone know how to take it from here? Help is much appreciated.
P.S.: This (unanswered) question did not help me either.
The only "solution" I could find was to re-install RStudio.
I recently installed pandoc 2.4 on Windows and the conversion failed with error 1 occurs for all knitting. I can't knit html, word, and pdf.
The error says
output file: template.knitmd
pandoc.exe: template.utf8.md: openBinaryFile: does not exist (No such file or directory)
Error: pandoc document conversion failed with error 1
Execusion halted
This happens to even the raw basic template rmd file.
I am using a closed network without internet connection and limited writing permission. Previously I was able to knit rmd files located in documents folder generating outputs in same location.
The sessionInfo() says
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: windows >=8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_collate=english_united states.1252 lc_ctype=english_united states.1252 lc_monetary=english_united states.1252
[4] LC_Numeric=C LC_TIME=english_united states.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] flextable_0.4.5 officer_0.3.2 knitr_1.20 rmarkdown_1.10
loaded via a namespace (and not attached):
[1] Rcpp_1.0.0 digest_0.6.18 rprojroot_1.3-2 R6_2.3.0 backports_1.1.2 magrittr_1.5 evaluate_0.12
[8]zip_1.0.0 stringi_1.2.4 gdtools_0.1.7 uuid_0.1-2 xml2_1.2.0 tools_3.5.1 stringr_1.3.1
[15] yaml_2.2.0 compiler_3.5.1 base64enc_0.1-3 htmltools_0.3.6
Any advice will be highly appreciated. (Or even ways how to change the settings back to old pandoc version without deleting the version 2.4.)
I have had this issue as well. Mapping the network drive where my R project was stored by following the instructions here solved the issue for me.
Facing problems with rmarkdown in Rstudio environment.
The following error is being reported:
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (MiKTeX 2.9)
log4cxx: No appender could be found for logger (pdflatex).
log4cxx: Please initialize the log4cxx system properly.
Sorry, but pdflatex did not succeed.
You may want to visit the MiKTeX project page (http://miktex.org), if you
need help.
I saw the same problem being reported by few others but did not find a proposed way to solve.
MikTex 2.9.5721 x64
pandoc 1.15.0.6
sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] devtools_1.8.0
loaded via a namespace (and not attached):
[1] R6_2.1.1 Rcpp_0.12.0 curl_0.9.3 digest_0.6.8 git2r_0.11.0 htmltools_0.2.6 httr_1.0.0 magrittr_1.5
[9] memoise_0.2.1 rmarkdown_0.8 rversions_1.0.2 stringi_0.5-5 stringr_1.0.0 tools_3.1.2 xml2_0.1.1 yaml_2.1.13
When I tried to generate with yo jhipster on Windows 7 32 bits machine, I got the below error:
bower json3#~3.2.5 progress received 3.7MB of 4.9MB
downloaded, 75% libjpeg-62.dll: downloading [===================]
100% 0.0s
? pre-build test failed, compiling from source...
d:\Self_jhipster\node_modules\grunt-contrib-imagemin\node_modules\jpegtran-bin\
lib\check.js:19
throw new Error('building is not supported on ' + process.platform);
^ Error: building is not supported on win32
at d:\Self_jhipster\node_modules\grunt-contrib-imagemin\node_modules\jpegtran-bin\lib\check.js:19:10
How to solve this error?
I'm the author of http://jhipster.github.io/ which is the generator your are referring to.
I have found your problem, it is indeed a bug in jpegtran-bin. I have updated all the dependencies in Grunt.js, and it should now work fine on Windows.
This will be commited in the next release (0.2.1), which should be out in a few hours.
You can also submit a bug at https://github.com/jhipster/generator-jhipster/issues
After google with more correct keywords, the solution from https://github.com/gruntjs/grunt-contrib-imagemin/issues/109 works for me.
In application's package.json, add "jpegtran-bin": "0.2.0" before
the reference for imagemin,
Remove node_module folder locally.
Run npm install again.