I am having trouble getting DeepWater up and running in R via H2O. I have downloaded the most recent .jar file ( I think) but I get the following error this install command:
install.packages("C:\\Users\\..\\Documents\\R\\win-
library\\3.4\\h2o_3.10.3.99999.tar.gz", repos = NULL, type = "source",
lib="C:\\Users\\..\\Documents\\R\\win-library\\3.4")
* installing *source* package 'h2o' ...
** R Error in .install_package_code_files(".", instdir) : files in 'C:/Users/.../AppData/Local/Temp/RtmpuyZ5fc/R.INSTALL3783508571d/h2o/R' missing from 'Collate' field: xgboost.R ERROR: unable to collate and parse R files for package 'h2o'
* removing 'C:/Users/.../Documents/R/win-library/3.4/h2o'
* restoring previous 'C:/Users/.../Documents/R/win-library/3.4/h2o' Warning in install.packages : running command '"C:/PROGRA~1/R/R-34~1.0/bin/x64/R" CMD INSTALL -l "C:\Users\...\Documents\R\win-library\3.4" "C:/Users/.../Documents/R/win-library/3.4/h2o_3.10.3.99999.tar.gz"' had status 1 Warning in install.packages : installation of package ‘C:/Users/.../Documents/R/win-library/3.4/h2o_3.10.3.99999.tar.gz’ had non-zero exit status Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) && : missing value where TRUE/FALSE needed
Yes we had some unused deps in one of our files in version 3.10.3.x, the one you're using.
It should be fixed in the newest version, which is 3.11.0.X and which you can get from here.
#Edit:
The above version was built for Linux, though - if you want to run it on windows you'll have to build it yourself according to the instructions here for deepwater and here for h2o. We don't have nightly builds for Windows just yet.
Related
I have some Affymetrix data that I would like to open using the read.affybatch() command in affy. I have downloaded the biocLite and affy packages with no issues, but as soon as I try and read my .CEL files using the read command it comes up with the following problem:
Library - package hgu133acdf not installed
Library - package hgu133acdf not installed
In addition: Warning messages:
1: In read.affybatch(filenames = "MonoHypo_U133A_04_12_03.CEL", "MonoC_U133A_04_12_03.CEL", :
Incompatible phenoData object. Created a new one.
2: running command '"C:/PROGRA~1/R/R-33~1.2/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.2\library" C:\windows\TEMP\RtmpKKBTXV/downloaded_packages/hgu133acdf_2.18.0.tar.gz' had status 1
3: In install.packages(cdfname, lib = lib, repos = biocinstallRepos(), :
installation of package ‘hgu133acdf’ had non-zero exit status
4: missing cdf environment! in show(AffyBatch)
5: running command '"C:/PROGRA~1/R/R-33~1.2/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.2\library" C:\windows\TEMP\RtmpKKBTXV/downloaded_packages/hgu133acdf_2.18.0.tar.gz' had status 1
6: In install.packages(cdfname, lib = lib, repos = biocinstallRepos(), :
installation of package ‘hgu133acdf’ had non-zero exit status
So, the issue seems to be this hgu133acdf package, but using the command from BioConductor to install this package I get the following error:
biocLite("hgu133acdf")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘hgu133acdf’
installing the source package ‘hgu133acdf’
trying URL 'https://bioconductor.org/packages/3.4/data/annotation/src/contrib/hgu133acdf_2.18.0.tar.gz'
Content type 'application/x-gzip' length 1732200 bytes (1.7 MB)
downloaded 1.7 MB
'\\filestore.soton.ac.uk\users\rl1e15\mydocuments\PhD\PhD Year 1 2016-2017\Analysis\In Silico\R\Hypoxia and Normoxia Monocytes'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows directory.
ERROR: unable to create 'C:/Program Files/R/R-3.3.2/library/hgu133acdf'
The downloaded source packages are in
‘C:\Windows\Temp\RtmpKKBTXV\downloaded_packages’
Warning messages:
1: running command '"C:/PROGRA~1/R/R-33~1.2/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.2\library" C:\windows\TEMP\RtmpKKBTXV/downloaded_packages/hgu133acdf_2.18.0.tar.gz' had status 1
2: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘hgu133acdf’ had non-zero exit status
I have tried installing hgu133acdf to my local drive using biocLite("hgu133acdf", lib="C:/Program Files/R/R-3.3.2/library") but the same non-zero exit status comes up. Sometimes it tells me I need to update nlme so I try that but the nlme_3.1-130 is not compatible with R-3-3-2 or when I update the package it still doesn't work.
So if anybody was curious, after hours of playing around with R I finally found the solution. As I have a work laptop, administrative rights are not automatically permitted, so I set the security of the directory all my packages download to to allow everything. I ran R as an administrator, installed all the necessary packages that kept flagging up when I tried the read.affybatch() command, and it worked!
I would like to use functions in the mvpart package in R. I know it has been removed from CRAN, but I tried installing archive versions available here: http://cran.r-project.org/web/packages/mvpart/index.html
install.packages("D:/mvpart_1.6-2.tar.gz", repos = NULL, type = "source")
I get this result:
Installing package into ‘C:/Users/jk/Documents/R/win-library/3.1’
(as ‘lib’ is unspecified)
* installing source package 'mvpart' ...
** package 'mvpart' successfully unpacked and MD5 sums checked
** libs
*** arch - i386
Warning: running command 'make -f "C:/PROGRA~1/R/R-31~1.3/etc/i386/Makeconf" -f "C:/PROGRA~1/R/R-31~1.3/share/make/winshlib.mk" SHLIB="mvpart.dll" OBJECTS="anova.o branch.o bsplit.o choose_surg.o dist.o fix_cp.o formatg.o free_tree.o gini.o graycode.o insert_split.o make_cp_list.o make_cp_table.o mrt.o mysort.o nodesplit.o partition.o poisson.o pred_rpart.o rpart.o rpart_callback.o rpartexp2.o rpcountup.o rpmatrix.o rundown.o rundown2.o s_to_rp.o s_xpred.o surrogate.o usersplit.o vgdist.o xdiss.o xval.o"' had status 127
ERROR: compilation failed for package 'mvpart'
* removing 'C:/Users/jk/Documents/R/win-library/3.1/mvpart'
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-31~1.3/bin/x64/R" CMD INSTALL -l "C:\Users\jk\Documents\R\win-library\3.1" "D:/mvpart_1.6-2.tar.gz"' had status 1
Warning in install.packages :
installation of package ‘D:/mvpart_1.6-2.tar.gz’ had non-zero exit status
My questions are: Did I do something wrong here - is there a way to install 'mvpart'? Or, is there another package that will do multivariate partitioning, similar to 'mvpart'?
Option 1:
An archive install must be compiled, as it's stored as source code. Probably, you have not installed the R Tools compiler for Windows. Follow the install instructions here.
Once that was done, for me, mvpart installed flawlessly from the downloaded archive:
install.packages("C:/mydownload/path/mvpart_1.6-2.tar.gz", repos = NULL, type = "source")
Option 2:
If Option 1 doesn't get the job done, get the devtools package:
install.packages("devtools")
Use it to get the github version:
devtools::install_github("cran/mvpart")
I believe you'll still need the R tools compiler though
downloading Xcode from either the Apple AppStore or Apple Developer website solved my issues installing mvpart. The app version required iOS 10.13 as of this post, but it was easy to find a compatible older version on the website to download. After you download it, move it to your Applications folder and then open it. After that then the devtools:::install_github() worked for me.
I tryed to install from file an old version of RgoogleMaps package with this command
install.packages("F://RgoogleMaps_1.1.9.15.tar.gz", repos = NULL, type="source")
but i found this error message:
* installing *source* package 'RgoogleMaps' ...
** package 'RgoogleMaps' successfully unpacked and MD5 sums checked
ERROR: a 'NAMESPACE' file is required
* removing 'C:/Users/Famiglia Mazza/Documents/R/win-library/3.1/RgoogleMaps'
* restoring previous 'C:/Users/Famiglia Mazza/Documents/R/win-library/3.1/RgoogleMaps'
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-31~1.2/bin/x64/R" CMD INSTALL -l "C:\Users\Famiglia Mazza\Documents\R\win-library\3.1" "F://RgoogleMaps_1.1.9.15.tar.gz"' had status 1
Warning in install.packages :
installation of package ‘F://RgoogleMaps_1.1.9.15.tar.gz’ had non-zero exit status
what can I do? I'm using R on Windows
In R 2.14.0 a requirement was made that all packages had namespaces, but as a transitional arrangement those that didn't would have one automatically generated at install time.
A package R code but without a ‘NAMESPACE’ file will have a default
one created at R CMD build or R CMD INSTALL time, so all packages will
be installed with namespaces. A consequence of this is that
.First.lib() functions need to be copied to .onLoad() (usually) or
.onAttach(). For the time being, if there is an auto-generated
‘NAMESPACE’ file and no .onLoad() nor .onAttach() function is found
but .First.lib() is, it will be run as the attach hook (unless the
package is one of a list of known exceptions, when it will be run as
the load hook).
However, by R 3.0.0 this transitional arrangement was ended:
The transitional support for installing packages without namespaces
(required since R 2.14.0) has been removed. R CMD build will still add
a namespace, but a .First.lib() function will need to be converted.
R CMD INSTALL no longer adds a namespace (so installation will fail),
and a .First.lib() function in a package will be ignored (with an
installation warning for now).
As an exception, packages without a ‘R’ directory and no ‘NAMESPACE’
file can still be installed.
Therefore, I suggest you use an older version of R to run this package. One prior to R 3.0.0 should suffice, and the latest one prior to that is R 2.15.3.
Did anyone tried to install R package: UScensus2010blk on your own PC?
I tried to use from UScensus2010:
install.blk ("windows")
It gives an error saying "Not Available Yet"
I downloaded the package myself (4.2GB!) and tried to install from local and I still get error messages:
installing source package 'UScensus2010blk' ...
** data
Warning in file.copy(files, is, TRUE) :
problem copying data\montana.blk10.rda to Q:\LCVDJ\R\R-3.0.2\library\UScensus2010blk\data\montana.blk10.rda: Invalid argument
...
(the error message repeats for different states)
...
** help
Error in lazyLoadDBinsertListElement(from, i, datafile, ascii, compress, :
write failed
ERROR: installing Rd objects failed for package 'UScensus2010blk'
* removing 'Q:/LCVDJ/R/R-3.0.2/library/UScensus2010blk'
Warning in install.packages :
running command '"Q:/LCVDJ/R/R-30~1.2/bin/i386/R" CMD INSTALL -l "Q:\LCVDJ\R\R-3.0.2\library" "C:/Users/n1304/Downloads/UScensus2010blk_1.00.tar.gz"' had status 1
Warning in install.packages :
installation of package ‘C:/Users/n1304/Downloads/UScensus2010blk_1.00.tar.gz’ had non-zero exit status
Does anyone have any idea why my installation is failed? I'm using R-3.0.2
Thanks!
There's an error in the census2010 package. The functions install.tract, install.blk, install.blkgrp, install.county, and install.cdp are supposed to check for R version >= 2.11 if you call the functions with the "windows" argument, but they only check the minor version so if you have R version 3.0 through 3.10 they incorrectly report an error.
To work around this error, you should be able to run
install.packages('UScensus2010blk', repos='http://lakshmi.calit2.uci.edu/census2000/R/', type='source')
instead of
install.blk('windows')
I tried to install it, and received the same message. It appears to be a problem with all the "windows" installations, as the command install.blk("linux") is functional.
I'm trying to install development version of ggbiplotfrom Github. During installation I'm getting the following error message:
library(devtools)
install_github("ggbiplot", "vqv")
Installing github repo(s) ggbiplot/master from vqv
Installing ggbiplot.zip from https://github.com/vqv/ggbiplot/zipball
Installing ggbiplot
* checking for file 'C:\Users\Muhammad Yaseen\AppData\Local\Temp\Rtmpsx4n5u\vqv-ggbiplot-2623d7c/DESCRIPTION' ... OK
* preparing 'ggbiplot':
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* looking to see if a 'data/datalist' file should be added
* building 'ggbiplot_0.5.tar.gz'
cygwin warning:
MS-DOS style path detected: C:/Users/MUHAMM~1/AppData/Local/Temp/Rtmpsx4n5u/ggbiplot_0.5.tar.gz
Preferred POSIX equivalent is: /cygdrive/c/Users/MUHAMM~1/AppData/Local/Temp/Rtmpsx4n5u/ggbiplot_0.5.tar.gz
CYGWIN environment variable option "nodosfilewarning" turns off this warning.
Consult the user's guide for more details about POSIX paths:
http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
Warning: invalid package 'Yaseen/R/win-library/2.14'
Error: ERROR: cannot cd to directory 'C:/Users/Muhammad'
Error: Command failed (1)
In addition: Warning message:
running command '"C:/PROGRA~1/R/R-214~1.2/bin/i386/R" CMD INSTALL C:\Users\MUHAMM~1\AppData\Local\Temp\Rtmpsx4n5u/ggbiplot_0.5.tar.gz --library=C:/Users/Muhammad Yaseen/R/win-library/2.14' had status 1
Any idea to figure out this problem. Thanks in advance for your help and time.
Edit
After downloading from Github, also tried
install.packages("vqv-ggbiplot-2623d7c.tar.gz", repos=NULL, type="source")
which produced this error message
Installing package(s) into ‘C:/Users/Muhammad Yaseen/R/win-library/2.14’
(as ‘lib’ is unspecified)
Error in untar2(tarfile, files, list, exdir) : unsupported entry type 'g'
Warning messages:
1: running command 'C:/PROGRA~1/R/R-214~1.2/bin/i386/R CMD INSTALL -l "C:/Users/Muhammad Yaseen/R/win-library/2.14" "vqv-ggbiplot-2623d7c.tar.gz"' had status 1
2: In install.packages("vqv-ggbiplot-2623d7c.tar.gz", repos = NULL, :
installation of package ‘vqv-ggbiplot-2623d7c.tar.gz’ had non-zero exit status
It's because your Rlib path has a space in it: C:/Users/Muhammad Yasseen/R/win-library/2.14.
See how in the first error log the warning message was
running command '"C:/PROGRA~1/R/R-214~1.2/bin/i386/R" CMD INSTALL
C:\Users\MUHAMM~1\AppData\Local\Temp\Rtmpsx4n5u/ggbiplot_0.5.tar.gz
--library=C:/Users/Muhammad Yaseen/R/win-library/2.14'
had status 1
In particular, the --library=C:/Users/Muhammad Yaseen/R/win-library/2.14.
This should be --library="C:/Users/Muhammad Yaseen/R/win-library/2.14" to deal with the space.
Using install.packages takes care of the quotes for you - see how your second warning message (when you used install.packages) was
running command 'C:/PROGRA~1/R/R-214~1.2/bin/i386/R CMD INSTALL
-l "C:/Users/Muhammad Yaseen/R/win-library/2.14"
"vqv-ggbiplot-2623d7c.tar.gz"' had status 1
The -l "C:/Users/Muhammad Yasseen/R/win-library/2.14" has quote marks around it, so you don't get the same error.
I had a quick look at the install-github sources, and it constructs the R CMD INSTALL command via:
paste("CMD INSTALL ", built_path, " --library=", .libPaths()[1], sep="")
See how it doesn't surround .libPaths()[1] by double quotes in case of spaces? I'd guess that's your problem.
As to a fix - there seems to be an error using install.packages() on a tar file generated by git (as reported here). So, you can either:
change your R library location to somewhere without spaces
unzip the .tar.gz file (I don't know what software does this on Windows) and install from the extracted directories rather than the .tar.gz.
You can't unzip the .tar.gz because it cleans up that file quicker than you can grab it (I've watched it appear and get deleted again). Correct me if I'm wrong, but I also can't get devtools from github for teh same reason :S