I'm trying to install the fastman function so I can make a manhattan plot. This is my code:
install.packages("remotes", repos = "http://cran.us.r-project.org", lib="/z/Comp/lu_group/Members/jwlorge/ATN/R")
remotes::install_github("danioreo/fastman",lib = "/z/Comp/lu_group/Members/jwlorge/ATN/R")
and this is my full error:
Error: package or namespace load failed for ‘fastman’ in namespaceExport(ns, exports):
undefined exports: fastman
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/z/Comp/lu_group/Members/jwlorge/ATN/R/fastman’
Warning message:
In i.p(...) :
installation of package ‘/tmp/RtmpP7Gtus/file129f63150195f8/fastman_0.1.0.tar.gz’ had non-zero exit status
I've been looking online for help and I haven't found many posts that are related to my problem, and none have solved the issue. I would greatly appreciate any help!
Alternatively, you can download the R scripts (https://github.com/danielldhwang/fastman/blob/master/R/fastman.R) and run source(fastman.R) from your R/RSudio session.
Source: https://github.com/danielldhwang/fastman/issues/2
Related
I'm trying to load the FRAPO package in RStudio but I keep getting the error message that it does not exist. During installation I get some warnings that the installation of the package had a non-zero exit status. How can I solve this issue?
I am getting the following error when I am loading a few libraries in R:
library(forecast)
Error : object ‘f_eval’ is not exported by 'namespace:lazyeval'
In addition: Warning message:
package ‘forecast’ was built under R version 3.3.2
Error: package or namespace load failed for ‘forecast’
library(tsoutliers)
Error : object ‘f_eval’ is not exported by 'namespace:lazyeval'
In addition: Warning message:
package ‘tsoutliers’ was built under R version 3.3.2
Error: package or namespace load failed for ‘tsoutliers’
I have tried reinstalling the packages but it didn't help. Also, I was able to use the forecast package previously but I started facing this error post the installation of tsoutliers package.
How can I resolve this issue?
This should do the job for you:
install.packages('lazyeval')
In the future, try and provide a bit more about your system and install, using the output from:
sessionInfo()
I've some problem to install package in R.
I write :
install.packages("rio", dependencies = TRUE)
And it gives the error message:
installing source package ‘rio’ ...
** package ‘rio’ correctement décompressé et sommes MD5 vérifiées
** R
** inst
** preparing package for lazy loading
Warning: S3 methods ‘[.labelled’, ‘[.labelled_spss’, ‘as.data.frame.labelled’, ‘as_factor.data.frame’, ‘as_factor.labelled’, ‘is.na.labelled_spss’, ‘print.labelled’, ‘print.labelled_spss’, ‘type_sum.labelled’, ‘zap_formats.data.frame’, ‘zap_formats.default’, ‘zap_labels.data.frame’, ‘zap_labels.default’, ‘zap_labels.labelled’, ‘zap_labels.labelled_spss’, ‘zap_missing.data.frame’, ‘zap_missing.default’, ‘zap_missing.labelled’, ‘zap_missing.labelled_spss’, ‘zap_widths.data.frame’, ‘zap_widths.default’ were declared in NAMESPACE but not found
Error in library.dynam(lib, package, package.lib) :
shared object ‘haven.so’ not found
ERROR: lazy loading failed for package ‘rio’
removing ‘/home/durand-s/R/x86_64-pc-linux-gnu-library/3.4/rio’
Warning in install.packages :
installation of package ‘/tmp/RtmpZI89tI/downloaded_packages/rio_0.4.6.tar.gz’ had non-zero exit status
I think that I miss some lib-dev or something like that but I cant find which one I need for rio's.
While trying to install the rio package in Microsoft windows. I faced an error. In order to resolve that issue, I googled and came to this page.
I know this post is a bit old but thought to share it for those who face a similar issue in installing this package.
Similar to this post:
Error: "there is no package called ..." and trying to use install.packages to solve it
I could only install rio when I used the command:
install.packages('rio', dependencies = TRUE, repos='http://cran.rstudio.com/')
This seems to be a Linux-specific problem (Got message unable to load shared object stats.so when R starts, shared object ‘RCurl.so’ not found)
Does uninstalling and reinstalling the havenpackage fix it?
Last week I upgraded from Ubuntu 14.04 to 14.10. The first time I've tried to use ggplot in RStudio since the update, I'm getting dependancy errors with my ggplot package and its no longer registered as installed (was working fine before). When I try to reinstal ggplot2:
install.packages("ggplot2",dep=TRUE)
The installation fails while trying to install the dependencies. Here's what the tail of the output looks like:
* installing *source* package ‘stringr’ ...
** package ‘stringr’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
Error in library.dynam(lib, package, package.lib) :
shared object ‘stringi.so’ not found
ERROR: lazy loading failed for package ‘stringr’
* removing ‘/home/james/R/x86_64-pc-linux-gnu-library/3.1/stringr’
Warning in install.packages :
installation of package ‘stringr’ had non-zero exit status
ERROR: dependency ‘stringr’ is not available for package ‘reshape2’
* removing ‘/home/james/R/x86_64-pc-linux-gnu-library/3.1/reshape2’
Warning in install.packages :
installation of package ‘reshape2’ had non-zero exit status
ERROR: dependency ‘reshape2’ is not available for package ‘ggplot2’
* removing ‘/home/james/R/x86_64-pc-linux-gnu-library/3.1/ggplot2’
Warning in install.packages :
installation of package ‘ggplot2’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpWNyAha/downloaded_packages’
I have a feeling this is the line (below) I should be looking at, but I'm not sure how to interprete this error, anyone have any suggestions for me? I really have no idea where to go from here, as I couldent find any other people experiencing the same error as me.
Error in library.dynam(lib, package, package.lib) :
shared object ‘stringi.so’ not found
Not sure if the Ubuntu upgrade I did relates to this... but I thought'd I'd mention it just in case.
Following #Nick Kennedey's comment, I tried installing stringi like this:
> install.packages("stringi",dep=TRUE)
Which resulted in this error I hadn't seen before:
2015-08-07 10:26:35 (256 KB/s) - ‘/tmp/RtmpQI4Uau/downloaded_packages/stringi_0.5-5.tar.gz’ saved [3639183/3639183]
ERROR: failed to lock directory ‘/home/james/R/x86_64-pc-linux-gnu-library/3.1’ for modifying
Try removing ‘/home/james/R/x86_64-pc-linux-gnu-library/3.1/00LOCK-stringi’
Warning in install.packages :
installation of package ‘stringi’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpQI4Uau/downloaded_packages’
> install.packages("stringi",dep=TRUE)
So the I followed the suggestion in the error an removed the LOCK folder.
In the terminal: rm -r /home/james/R/x86_64-pc-linux-gnu-library/3.1/00LOCK-stringi’
Then tried installing the stringi package again, and it worked! This was the issue... now I've just finished installing with no issues.
I am still a little bit confused though... as to how this error can come about. Any ideas on what causes this so I can avoid it in the future? Is it possible it was a symptom of my recent upgrade to 14.10?
Got the same error while installing install.packages("knitr")
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/usr/local/lib/R/site-library/stringi/libs/stringi.so'
I solved it by doing the below:
In Ubuntu 16.04 and above
sudo apt install r-cran-stringi
In earlier versions (which had apt-get)
sudo apt-get install r-cran-stringi
In my case I solved the problem through installing stringi and ggplot2 from the terminal of linux. The problem has some relation with RStudio.
Hope somebody could help me .. I'm trying to install the mzmatch.R package for metabolomics, following the instructions here: http://mzmatch.sourceforge.net/tutorial.mzmatch.r.php
I'm completely new to R so this is my first time doing this sort of thing. First, I downloaded the latest version of R and installed it on Mac OSX 10.7. This is the version of R that I have running:
R 2.15.0 GUI 1.51 Leopard build 64-bit (6148)
Then I launched R64.app and typed the following commands (as specified in the instructions in the link above) to install the package and all its dependencies.
> source("http://bioconductor.org/biocLite.R")
> biocLite(c("faahKO", "xcms", "multtest"))
> install.packages(c("rJava","XML","snow","caTools","bitops","ptw"))
> source ("http://puma.ibls.gla.ac.uk/mzmatch.R/install_mzmatch.R")
The last step will always fail with the following message:
trying URL 'http://puma.ibls.gla.ac.uk/mzmatch.R/mzmatch.R.tar.gz'
Content type 'application/x-gzip' length 104535 bytes (102 Kb)
opened URL
==================================================
downloaded 102 Kb
* installing *source* package ‘mzmatch.R’ ...
** R
** preparing package for lazy loading
Error : .onLoad failed in loadNamespace() for 'mzR', details:
call: value[[3L]](cond)
error: failed to load module Ramp from package mzR
could not find function "errorOccured"
Error : package ‘mzR’ could not be loaded
ERROR: lazy loading failed for package ‘mzmatch.R’
* removing ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/mzmatch.R’
Warning message:
In install.packages(pkgs = "mzmatch.R.tar.gz", repos = NULL, type = "source") :
installation of package ‘mzmatch.R.tar.gz’ had non-zero exit status
I thought this was because the library "mzR" cannot be loaded, so I tried:
> biocLite("mzR")
> library("mzR")
and sure enough, the same error appeared:
Loading required package: Rcpp
Error : .onLoad failed in loadNamespace() for 'mzR', details:
call: value[[3L]](cond)
error: failed to load module Ramp from package mzR
could not find function "errorOccured"
Error: package/namespace load failed for ‘mzR’
I'm quite lost now, and not sure what to do at all. Thanks for reading !
Assuming you are running mzR v1.2.1 and Rcpp v0.9.12, the problem you see is an unfortunate and unexpected incompatibility between the two. In the meantime, downgrading to Rcpp_0.9.10.zip will fix the issue. Hope to commit a proper fix soon.
Laurent
UDAPE: The issue was the result of compiler/linker error and required a fresh mzR build, which is now available through biocLite.