Error loading "oligo" Bioconductor package - r

On Windows XP, After updating to R 2.15.3 and updating all libraries, I was no longer able to load the "oligo" package from BioConductor.
To recreate:
source("http://bioconductor.org/biocLite.R") #install the BioC installer
biocLite("oligo") #download and install the oligo package
library("oligo") #attempt to load
Gets the following error:
Error in inDL(x, as.logical(local), as.logical(now), ...) :
unable to load shared object 'C:/Program Files/R/R-2.15.3/library/affxparser/libs/i386/affxparser.dll':
LoadLibrary failure: The specified procedure could not be found.
The file it mentions, "C:/Program Files/R/R-2.15.3/library/affxparser/libs/i386/affxparser.dll", is right where it's supposed to be.
sessionInfo() returns:
R version 2.15.3 (2013-03-01)
Platform: i386-w64-mingw32/i386 (32-bit)
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
other attached packages:
[1] Biobase_2.18.0 oligoClasses_1.20.0 BiocGenerics_0.4.0
loaded via a namespace (and not attached):
[1] affyio_1.26.0 BiocInstaller_1.8.3 Biostrings_2.26.3
[4] bit_1.1-10 codetools_0.2-8 ff_2.2-11
[7] foreach_1.4.0 GenomicRanges_1.10.7 IRanges_1.16.6
[10] iterators_1.0.6 parallel_2.15.3 stats4_2.15.3
[13] tools_2.15.3 zlibbioc_1.4.0
.libPaths() returns:
[1] "C:/Program Files/R/R-2.15.3/library"
[2] "C:/Program Files/RStudio/R/library"

Related

install_github R issue, SSL connect error

I am trying to install a package from github in R but am getting an error I havent been able to solve.
>devtools::install_github("hadley/multidplyr")
Downloading GitHub repo hadley/multidplyr#master
Error in curl::curl_fetch_memory(url, handle = handle) :
SSL connect error
This is on a 64bit Windows 7 enterprise machine. I tried to turn off verificaiton of the peer's ssl certificate with the following:
set_config( config( ssl_verifypeer = 0L ) )
This didn't change the error message unfortunately. Any help would be greatly appreciated.
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
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
[7] base
other attached packages:
[1] httr_1.0.0
loaded via a namespace (and not attached):
[1] R6_2.1.1 magrittr_1.5 tools_3.2.2 curl_0.9.4
[5] memoise_0.2.1 stringi_1.0-1 stringr_1.0.0 digest_0.6.8
[9] devtools_1.9.1

Can not install shinyTable successfully

I followed the instruction on the Github. It returned me an error like this:
install_github("shinyTable", "trestletech")
Downloading github repo trestletech/shinyTable#master
Error in curl::curl_fetch_memory(url, handle = handle) :
Timeout was reached
In addition: Warning message:
Username parameter is deprecated. Please use trestletech/shinyTable
Then, I tried to download the repo zip file and installed the shinyTable from local zip file in R studio. After that, I library(shinyTable). It return me an error.
> install.packages("D:/UserData/xxxx/Downloads/shinyTable-master.zip", repos = NULL)
Installing package into ‘D:/UserData/xxxx/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
> library(shinyTable)
Error in library(shinyTable) : there is no package called ‘shinyTable’
This is sessionInfo() result:
R version 3.2.1 (2015-06-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] shinyRGL_0.1.0 devtools_1.8.0 rJava_0.9-7
loaded via a namespace (and not attached):
[1] rgl_0.95.1247 Rcpp_0.12.0 digest_0.6.8 mime_0.3 R6_2.1.0 xtable_1.7-4 git2r_0.10.1
[8] magrittr_1.5 httr_1.0.0 stringi_0.5-5 curl_0.9.2 xml2_0.1.1 tools_3.2.1 stringr_1.0.0
[15] shiny_0.12.2 httpuv_1.3.3 rversions_1.0.2 htmltools_0.2.6 tcltk_3.2.1 memoise_0.2.1
Does anyone know the reason and tell me how to install it? Thank you.
I had similar issues recently. Can you try this:
library(devtools)
install_git("https://github.com/trestletech/shinyTable")

lme4/Matrix: Entry Point Not Found - how to fix?

I have been using lme4 every day for quite a while.
Today, after opening R (x64 v 2.15.1), it complained that there is no package called ‘lme4’. So I re-installed it.
When I ran require(lme4) a popup was generated saying Entry Point Not Found. The procedure entry point Rf_copyListMatrix could not be location in the dynamic link library R.dll and after clicking OK the message there was an error in the R console:
Error: package ‘Matrix’ could not be loaded
So I reinstalled Matrix, after running require(Matrix) the same popup is generated followed by this error in the console
Error in inDL(x, as.logical(local), as.logical(now), ...) :
unable to load shared object 'C:/R/R-2.15.1/library/Matrix/libs/x64/Matrix.dll':
LoadLibrary failure: The specified procedure could not be found.
I have tried restarting R and rebooting the PC.
How can I fix this ?
Update:
sessionInfo() gives the following:
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United Kingdom.1252
[2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] lattice_0.20-10
loaded via a namespace (and not attached):
[1] grid_2.15.1
I have now solved this problem.
It required a minor upgrade of R from v 2.15.1 to 2.15.2

Installation error of slidifyLibraries from github

I installed slidify following instructions from here. I installed the windows binaries and started a slidify.rmd file successfully, but I could not install the slidifyLibraries, which makes the build crash. This is the error that follows:
* checking for file 'C:\Users\Roger\AppData\Local\Temp\RtmpYrHr6k\ramnathv-slidifyLibraries-8e8e781/DESCRIPTION' ... OK
* preparing 'slidifyLibraries':
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'slidifyLibraries_0.1.tar.gz'
ERROR
packaging into .tar.gz failed
Error: Command failed (1)
In addition: Warning message:
running command '"C:/NEWPRO~1/R-215~1.2/bin/x64/R" --vanilla CMD build "C:\Users\Roger\AppData\Local\Temp\RtmpYrHr6k\ramnathv-slidifyLibraries-8e8e781" --no-manual --no-resave-data' had status 1
When installing Rtools I was directed to install them directly from cran, which I did. This is the session info:
R version 2.15.2 (2012-10-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
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
[6] methods base
other attached packages:
[1] slidify_0.3.1
loaded via a namespace (and not attached):
[1] digest_0.6.0 evaluate_0.4.3 formatR_0.7
[4] knitr_0.9 markdown_0.5.3 stringr_0.6.2
[7] tools_2.15.2 whisker_0.1 yaml_2.1.5

R.matlab package appears corrupted

Solution: The package R.oo used by R.matlab has a function called getDate. I was loading --another function getDate() before loading the R.matlab package.
I can't load the R package R.matlab
Anyone has the same issue? I have the following error message:
Loading required package: R.matlab
Error in as.POSIXlt.POSIXct(x, tz) : invalid 'tz' value
Error: package 'R.matlab' could not be loaded
Edit: it happens since the last update on 3rd of Feb 2011
> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] grDevices datasets splines graphics stats tcltk utils methods base
other attached packages: [1] R.oo_1.7.5 R.methodsS3_1.2.1 waveslim_1.6.4 timeDate_2130.91 ncdf_1.6.5 rgl_0.92.798
[7] fields_6.3 spam_0.23-0 splancs_2.01-27 sp_0.9-76 maps_2.1-5 shapefiles_0.6
[13] foreign_0.8-41 scrapeR_0.1.6 XML_3.2-0.2 mFilter_0.1-3 RCurl_1.5-0.1 bitops_1.0-4.1
[19] outliers_0.14 chron_2.3-39 lmtest_0.9-27 PerformanceAnalytics_1.0.3.2 RODBC_1.3-2 quantmod_0.3-15
[25] TTR_0.20-2 xts_0.7-5 zoo_1.6-4 Defaults_1.1-1 rcom_2.2-3.1 rscproxy_1.3-1
[31] svSocket_0.9-51 TinnR_1.0.3 R2HTML_2.2 Hmisc_3.8-3 survival_2.36-2
loaded via a namespace (and not attached):
[1] cluster_1.13.2 grid_2.12.1 lattice_0.19-17 svMisc_0.9-61 tools_2.12.1
That's not an issue with R.matlab, but with something else. I see that it says "loading required package: R.matlab" , so the command came from somewhere else.
> library(R.matlab)
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.2.1 (2010-09-18) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.7.5 (2011-02-01) successfully loaded. See ?R.oo for help.
R.matlab v1.3.7 (2011-02-01) successfully loaded. See ?R.matlab for help.
On Windows 7, R 2.12.1.
Please provide the full detail of the command you used that loaded R.matlab. And you might want to post this on the R-help list or R-devel list, this seems to be a bug of some kind. It's always a good idea to put the package maintainer in cc, so they know.
Session info :
> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: i386-pc-mingw32/i386 (32-bit)
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] grid grDevices datasets splines graphics stats tcltk utils methods base
other attached packages:
[1] R.matlab_1.3.7 R.oo_1.7.5 R.methodsS3_1.2.1 reshape_0.8.3 plyr_1.2.1 gplots_2.8.0
[7] caTools_1.11 bitops_1.0-4.1 gdata_2.8.1 gtools_2.6.2 RColorBrewer_1.0-2 chron_2.3-39
[13] xlsReadWrite_1.5.3 svSocket_0.9-51 TinnR_1.0.3 R2HTML_2.2 Hmisc_3.8-3 survival_2.36-2
loaded via a namespace (and not attached):
[1] cluster_1.13.2 lattice_0.19-13 svMisc_0.9-61 tools_2.12.1
Solution: The package R.oo used by R.matlab has a function called getDate. I was loading --another function getDate() before loading the R.matlab package.

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