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nickflowcyto
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@nickflowcyto-13105
Last seen 7.1 years ago
Hey everyone,
I just started on bioconductor but have been using R for some time now. This error message pops up every time I reopen R, and try to load flowCore, flowViz, and flowStats.
>library("flowStats", lib.loc="~/R/win-library/3.4")
Loading required package: flowCore
Error: package or namespace load failed for ‘flowCore’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘Rcpp’
Error: package ‘flowCore’ could not be loaded
I checked the versions with BiocInstaller::biocValid() and came back true.
Thanks for any help, it is greatly appreciated!!
Nick
It is a little unusual to specify lib.loc for library; if Rcpp were installed in a different library (e.g., by your system administrator, or by a different you) then it wouldn't be found. Also, how did you install flowStats? If using
BiocInstaller::biocLite("flowStats")(the recommended way) then R would (should?) have installed the Rcpp dependency if it were not already available.Hi Martin,
Thanks for the reply! I did install flowStats via biocLite("flowStats") through the same user. I just re-ran the bioInstaller code source("https://bioconductor.org/biocLite.R"),, the system asked to update packages, but after quitting the R session and beginning again, the same message came up. Do the bioconductor packages normally work without a reinstallation every time? Thanks again, I really appreciate it.
No need to re-install each time. Did you try and install Rcpp, BiocInstaller::biocLite("Rcpp") ? Does it install successfully? It's not so helpful to say 'the same message came up', better to copy / paste the exact transcript of what you do / what R says (for long installations it is sometimes necessary to trim the transcript, but somehow ironically whenever people trim the transcript they remove the most important part...). Also provide the output of sessionInfo()
Rcpp was successful however flowStats still was not. Here is the full transcript with session info.
BiocInstaller::biocLite("Rcpp") BioC_mirror: https://bioconductor.org Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21). Installing package(s) ‘Rcpp’ trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/Rcpp_0.12.11.zip' Content type 'application/zip' length 3380155 bytes (3.2 MB) downloaded 3.2 MB package ‘Rcpp’ successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\nickcomp\downloaded_packages installation path not writeable, unable to update packages: foreign, Matrix > biocLite(flowStats) Error in biocLite(flowStats) : could not find function "biocLite" > sessionInfo() R version 3.4.0 (2017-04-21) 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 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] compiler_3.4.0 BiocInstaller_1.26.0 tools_3.4.0And the full transcript for BiocInstaller::biocLite("flowStats") ?
>BiocInstaller::biocLite("flowStats")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21).
Installing package(s) ‘flowStats’
trying URL 'https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/flowStats_3.34.0.zip'
Content type 'application/zip' length 8752749 bytes (8.3 MB)
downloaded 8.3 MB
package ‘flowStats’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\nickcomp\downloaded_packages
installation path not writeable, unable to update packages: foreign, Matrix
> sessionInfo()
R version 3.4.0 (2017-04-21)
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
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.4.0 BiocInstaller_1.26.0 tools_3.4.0
Isn't this a re-download?
Yes, you did just download and install flowStats again, and normally it would not be necessary. But this is the first time the transcript of the session has been shared with others.
So can you now provide the full transcript of
library(flowStats) .libPaths() c("flowStats", "Rcpp") %in% dir(.libPaths())If loading flowStats fails, could you also try (and report) the results of
library(Rcpp) library(flowStats) packageDescription("Rcpp") packageDescription("flowStats")Martin,
As a new user I had reached my reply limit yesterday. Here is the transcript, flowStats now works! Thank you for your help! I think the missing link was the
BiocInstaller::biocLite("Rcpp")earlier.> library(flowStats) Loading required package: fda Loading required package: splines Loading required package: Matrix Attaching package: ‘Matrix’ The following object is masked from ‘package:flowCore’: %&% Attaching package: ‘fda’ The following object is masked from ‘package:graphics’: matplot Loading required package: cluster Loading required package: flowWorkspace Loading required package: ncdfFlow Loading required package: RcppArmadillo Loading required package: BH > .libPaths() [1] "C:/Users/nickcomp/Documents/R/win-library/3.4" [2] "C:/Program Files/R/R-3.4.0/library" > c("flowStats", "Rcpp") %in% dir(.libPaths()) [1] TRUE TRUE