Can't install caret package in R
I have tried multiple ways to install the caret package in R.
The error message that I receive is as follows:
Error: package or namespace load failed for ‘caret’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘dimRed’
When I try to install dimRed, I get the following message:
Installing package into ‘C:/Users/Thomas/Documents/R/win-library/3.4’
(as ‘lib’ is unspecified)
Warning in install.packages :
dependency ‘Biobase’ is not available
There is a binary version available but the source version is later:
binary source needs_compilation
dimRed 0.1.0 0.2.1 FALSE
installing the source package ‘dimRed’
trying URL 'https://cran.rstudio.com/src/contrib/dimRed_0.2.1.tar.gz'
Content type 'application/x-gzip' length 363025 bytes (354 KB)
downloaded 354 KB
ERROR: dependency 'Biobase' is not available for package 'dimRed'
* removing 'C:/Users/Thomas/Documents/R/win-library/3.4/dimRed'
In R CMD INSTALL
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-34~1.4/bin/x64/R" CMD INSTALL -l "C:UsersThomasDocumentsRwin-library3.4" C:UsersThomasAppDataLocalTempRtmpqKhsKn/downloaded_packages/dimRed_0.2.1.tar.gz' had status 1
Warning in install.packages :
installation of package ‘dimRed’ had non-zero exit status
The downloaded source packages are in
‘C:UsersThomasAppDataLocalTempRtmpqKhsKndownloaded_packages’
Per previous posts, I have updated RStudio. I have attempted an install from install_url.
Any suggestions are welcome.
r rstudio r-caret
edited Nov 13 '18 at 10:51
Tjebo
2,3531327
asked Nov 13 '18 at 0:44
coultcoult
161
add a comment |
I have tried multiple ways to install the caret package in R.
The error message that I receive is as follows:
Error: package or namespace load failed for ‘caret’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘dimRed’
When I try to install dimRed, I get the following message:
Installing package into ‘C:/Users/Thomas/Documents/R/win-library/3.4’
(as ‘lib’ is unspecified)
Warning in install.packages :
dependency ‘Biobase’ is not available
There is a binary version available but the source version is later:
binary source needs_compilation
dimRed 0.1.0 0.2.1 FALSE
installing the source package ‘dimRed’
trying URL 'https://cran.rstudio.com/src/contrib/dimRed_0.2.1.tar.gz'
Content type 'application/x-gzip' length 363025 bytes (354 KB)
downloaded 354 KB
ERROR: dependency 'Biobase' is not available for package 'dimRed'
* removing 'C:/Users/Thomas/Documents/R/win-library/3.4/dimRed'
In R CMD INSTALL
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-34~1.4/bin/x64/R" CMD INSTALL -l "C:UsersThomasDocumentsRwin-library3.4" C:UsersThomasAppDataLocalTempRtmpqKhsKn/downloaded_packages/dimRed_0.2.1.tar.gz' had status 1
Warning in install.packages :
installation of package ‘dimRed’ had non-zero exit status
The downloaded source packages are in
‘C:UsersThomasAppDataLocalTempRtmpqKhsKndownloaded_packages’
Per previous posts, I have updated RStudio. I have attempted an install from install_url.
Any suggestions are welcome.
r rstudio r-caret
edited Nov 13 '18 at 10:51
Tjebo
2,3531327
asked Nov 13 '18 at 0:44
coultcoult
161
1
Have you tried installingbiobasefirst? See the documentation for installation help
– CIAndrews
Nov 13 '18 at 0:52
These are confusing messages. Biobase is a Bioconductor package. Neither it, nor dimRed seem to be required for caret, according to its CRAN page. It sounds like your current R environment is just messed up. I would restart R and try again.
– neilfws
Nov 13 '18 at 0:56
It's possible that one of the package required bycaret(and there are a big boatload of them) does havedimRedas a dependency. I just installedcaretand dimRed was installed during the dependencies phase. Si suggestions to reinstall my be a waste of time. (I did already have Biobase installed.)
– 42-
Nov 13 '18 at 1:43
I ran install.packages("dimRed", dependencies = T) and now my base error message has changed to - > library("caret") Error: package or namespace load failed for ‘caret’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘Biobase’. When I try to install Biobase, I'm told that it is not available on R3.4.4. Any ideas?
– coult
Nov 13 '18 at 2:38
add a comment |
I have tried multiple ways to install the caret package in R.
The error message that I receive is as follows:
Error: package or namespace load failed for ‘caret’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘dimRed’
When I try to install dimRed, I get the following message:
Installing package into ‘C:/Users/Thomas/Documents/R/win-library/3.4’
(as ‘lib’ is unspecified)
Warning in install.packages :
dependency ‘Biobase’ is not available
There is a binary version available but the source version is later:
binary source needs_compilation
dimRed 0.1.0 0.2.1 FALSE
installing the source package ‘dimRed’
trying URL 'https://cran.rstudio.com/src/contrib/dimRed_0.2.1.tar.gz'
Content type 'application/x-gzip' length 363025 bytes (354 KB)
downloaded 354 KB
ERROR: dependency 'Biobase' is not available for package 'dimRed'
* removing 'C:/Users/Thomas/Documents/R/win-library/3.4/dimRed'
In R CMD INSTALL
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-34~1.4/bin/x64/R" CMD INSTALL -l "C:UsersThomasDocumentsRwin-library3.4" C:UsersThomasAppDataLocalTempRtmpqKhsKn/downloaded_packages/dimRed_0.2.1.tar.gz' had status 1
Warning in install.packages :
installation of package ‘dimRed’ had non-zero exit status
The downloaded source packages are in
‘C:UsersThomasAppDataLocalTempRtmpqKhsKndownloaded_packages’
Per previous posts, I have updated RStudio. I have attempted an install from install_url.
Any suggestions are welcome.
r rstudio r-caret
edited Nov 13 '18 at 10:51
Tjebo
2,3531327
asked Nov 13 '18 at 0:44
coultcoult
161
I have tried multiple ways to install the caret package in R.
The error message that I receive is as follows:
Error: package or namespace load failed for ‘caret’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘dimRed’
When I try to install dimRed, I get the following message:
Installing package into ‘C:/Users/Thomas/Documents/R/win-library/3.4’
(as ‘lib’ is unspecified)
Warning in install.packages :
dependency ‘Biobase’ is not available
There is a binary version available but the source version is later:
binary source needs_compilation
dimRed 0.1.0 0.2.1 FALSE
installing the source package ‘dimRed’
trying URL 'https://cran.rstudio.com/src/contrib/dimRed_0.2.1.tar.gz'
Content type 'application/x-gzip' length 363025 bytes (354 KB)
downloaded 354 KB
ERROR: dependency 'Biobase' is not available for package 'dimRed'
* removing 'C:/Users/Thomas/Documents/R/win-library/3.4/dimRed'
In R CMD INSTALL
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-34~1.4/bin/x64/R" CMD INSTALL -l "C:UsersThomasDocumentsRwin-library3.4" C:UsersThomasAppDataLocalTempRtmpqKhsKn/downloaded_packages/dimRed_0.2.1.tar.gz' had status 1
Warning in install.packages :
installation of package ‘dimRed’ had non-zero exit status
The downloaded source packages are in
‘C:UsersThomasAppDataLocalTempRtmpqKhsKndownloaded_packages’
Per previous posts, I have updated RStudio. I have attempted an install from install_url.
Any suggestions are welcome.
r rstudio r-caret
r rstudio r-caret
edited Nov 13 '18 at 10:51
Tjebo
2,3531327
asked Nov 13 '18 at 0:44
coultcoult
161
edited Nov 13 '18 at 10:51
Tjebo
2,3531327
asked Nov 13 '18 at 0:44
coultcoult
161
edited Nov 13 '18 at 10:51
Tjebo
2,3531327
edited Nov 13 '18 at 10:51
Tjebo
2,3531327
edited Nov 13 '18 at 10:51
Tjebo
2,3531327
2,3531327
asked Nov 13 '18 at 0:44
coultcoult
161
asked Nov 13 '18 at 0:44
coultcoult
161
asked Nov 13 '18 at 0:44
coultcoult
161
161
1
Have you tried installingbiobasefirst? See the documentation for installation help
– CIAndrews
Nov 13 '18 at 0:52
These are confusing messages. Biobase is a Bioconductor package. Neither it, nor dimRed seem to be required for caret, according to its CRAN page. It sounds like your current R environment is just messed up. I would restart R and try again.
– neilfws
Nov 13 '18 at 0:56
It's possible that one of the package required bycaret(and there are a big boatload of them) does havedimRedas a dependency. I just installedcaretand dimRed was installed during the dependencies phase. Si suggestions to reinstall my be a waste of time. (I did already have Biobase installed.)
– 42-
Nov 13 '18 at 1:43
I ran install.packages("dimRed", dependencies = T) and now my base error message has changed to - > library("caret") Error: package or namespace load failed for ‘caret’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘Biobase’. When I try to install Biobase, I'm told that it is not available on R3.4.4. Any ideas?
– coult
Nov 13 '18 at 2:38
add a comment |
1
Have you tried installingbiobasefirst? See the documentation for installation help
– CIAndrews
Nov 13 '18 at 0:52
These are confusing messages. Biobase is a Bioconductor package. Neither it, nor dimRed seem to be required for caret, according to its CRAN page. It sounds like your current R environment is just messed up. I would restart R and try again.
– neilfws
Nov 13 '18 at 0:56
It's possible that one of the package required bycaret(and there are a big boatload of them) does havedimRedas a dependency. I just installedcaretand dimRed was installed during the dependencies phase. Si suggestions to reinstall my be a waste of time. (I did already have Biobase installed.)
– 42-
Nov 13 '18 at 1:43
I ran install.packages("dimRed", dependencies = T) and now my base error message has changed to - > library("caret") Error: package or namespace load failed for ‘caret’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘Biobase’. When I try to install Biobase, I'm told that it is not available on R3.4.4. Any ideas?
– coult
Nov 13 '18 at 2:38
1
1
Have you tried installing
biobase first? See the documentation for installation help– CIAndrews
Nov 13 '18 at 0:52
Have you tried installing
biobase first? See the documentation for installation help– CIAndrews
Nov 13 '18 at 0:52
These are confusing messages. Biobase is a Bioconductor package. Neither it, nor dimRed seem to be required for caret, according to its CRAN page. It sounds like your current R environment is just messed up. I would restart R and try again.
– neilfws
Nov 13 '18 at 0:56
These are confusing messages. Biobase is a Bioconductor package. Neither it, nor dimRed seem to be required for caret, according to its CRAN page. It sounds like your current R environment is just messed up. I would restart R and try again.
– neilfws
Nov 13 '18 at 0:56
It's possible that one of the package required by
caret(and there are a big boatload of them) does have dimRed as a dependency. I just installed caret and dimRed was installed during the dependencies phase. Si suggestions to reinstall my be a waste of time. (I did already have Biobase installed.)– 42-
Nov 13 '18 at 1:43
It's possible that one of the package required by
caret(and there are a big boatload of them) does have dimRed as a dependency. I just installed caret and dimRed was installed during the dependencies phase. Si suggestions to reinstall my be a waste of time. (I did already have Biobase installed.)– 42-
Nov 13 '18 at 1:43
I ran install.packages("dimRed", dependencies = T) and now my base error message has changed to - > library("caret") Error: package or namespace load failed for ‘caret’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘Biobase’. When I try to install Biobase, I'm told that it is not available on R3.4.4. Any ideas?
– coult
Nov 13 '18 at 2:38
I ran install.packages("dimRed", dependencies = T) and now my base error message has changed to - > library("caret") Error: package or namespace load failed for ‘caret’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘Biobase’. When I try to install Biobase, I'm told that it is not available on R3.4.4. Any ideas?
– coult
Nov 13 '18 at 2:38
add a comment |
2 Answers
2
active
oldest
votes
I was able to figure this out.
Simply typing install.packages won't work. In order to install Biobase, you have to run the following code in R console:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Biobase", version = "3.8")
More info: https://bioconductor.org/packages/release/bioc/html/Biobase.html
Once this step is done, I installed caret again using
install.packages("caret",dependencies = T)
And then it worked.
answered Nov 13 '18 at 3:15
user2730749user2730749
311
I have had the same issue as the questioner. I attempted this and once I triedlibrary(caret)I got the same 1st error as the questioner.
– a.powell
Nov 13 '18 at 18:25
Maybe it has something to do with the R version, as pointed out by a previous response. I was using R version 3.5.1 (2018-07-02) under Windows 10 Pro. And I used install.packages("caret",dependencies = T). You can try this out and see if there are any dependencies other than the Biobase package for caret.
– user2730749
Nov 18 '18 at 3:47
add a comment |
Warning ...
install.packages("BiocManager")
This only works if your R version is >= 3.5.0
for info I've the same problem under a Centos and a Windows.
issue solved on the windows with 3.5.1 R version. Not yet solved on the centOS (3.4.2)
answered Nov 13 '18 at 10:13
G. XibG. Xib
12
add a comment |
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2 Answers
2
active
oldest
votes
2 Answers
2
active
oldest
votes
active
oldest
votes
active
oldest
votes
I was able to figure this out.
Simply typing install.packages won't work. In order to install Biobase, you have to run the following code in R console:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Biobase", version = "3.8")
More info: https://bioconductor.org/packages/release/bioc/html/Biobase.html
Once this step is done, I installed caret again using
install.packages("caret",dependencies = T)
And then it worked.
answered Nov 13 '18 at 3:15
user2730749user2730749
311
I have had the same issue as the questioner. I attempted this and once I triedlibrary(caret)I got the same 1st error as the questioner.
– a.powell
Nov 13 '18 at 18:25
Maybe it has something to do with the R version, as pointed out by a previous response. I was using R version 3.5.1 (2018-07-02) under Windows 10 Pro. And I used install.packages("caret",dependencies = T). You can try this out and see if there are any dependencies other than the Biobase package for caret.
– user2730749
Nov 18 '18 at 3:47
add a comment |
I was able to figure this out.
Simply typing install.packages won't work. In order to install Biobase, you have to run the following code in R console:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Biobase", version = "3.8")
More info: https://bioconductor.org/packages/release/bioc/html/Biobase.html
Once this step is done, I installed caret again using
install.packages("caret",dependencies = T)
And then it worked.
answered Nov 13 '18 at 3:15
user2730749user2730749
311
I have had the same issue as the questioner. I attempted this and once I triedlibrary(caret)I got the same 1st error as the questioner.
– a.powell
Nov 13 '18 at 18:25
Maybe it has something to do with the R version, as pointed out by a previous response. I was using R version 3.5.1 (2018-07-02) under Windows 10 Pro. And I used install.packages("caret",dependencies = T). You can try this out and see if there are any dependencies other than the Biobase package for caret.
– user2730749
Nov 18 '18 at 3:47
add a comment |
I was able to figure this out.
Simply typing install.packages won't work. In order to install Biobase, you have to run the following code in R console:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Biobase", version = "3.8")
More info: https://bioconductor.org/packages/release/bioc/html/Biobase.html
Once this step is done, I installed caret again using
install.packages("caret",dependencies = T)
And then it worked.
answered Nov 13 '18 at 3:15
user2730749user2730749
311
I was able to figure this out.
Simply typing install.packages won't work. In order to install Biobase, you have to run the following code in R console:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Biobase", version = "3.8")
More info: https://bioconductor.org/packages/release/bioc/html/Biobase.html
Once this step is done, I installed caret again using
install.packages("caret",dependencies = T)
And then it worked.
answered Nov 13 '18 at 3:15
user2730749user2730749
311
answered Nov 13 '18 at 3:15
user2730749user2730749
311
answered Nov 13 '18 at 3:15
user2730749user2730749
311
answered Nov 13 '18 at 3:15
user2730749user2730749
311
311
I have had the same issue as the questioner. I attempted this and once I triedlibrary(caret)I got the same 1st error as the questioner.
– a.powell
Nov 13 '18 at 18:25
Maybe it has something to do with the R version, as pointed out by a previous response. I was using R version 3.5.1 (2018-07-02) under Windows 10 Pro. And I used install.packages("caret",dependencies = T). You can try this out and see if there are any dependencies other than the Biobase package for caret.
– user2730749
Nov 18 '18 at 3:47
add a comment |
I have had the same issue as the questioner. I attempted this and once I triedlibrary(caret)I got the same 1st error as the questioner.
– a.powell
Nov 13 '18 at 18:25
Maybe it has something to do with the R version, as pointed out by a previous response. I was using R version 3.5.1 (2018-07-02) under Windows 10 Pro. And I used install.packages("caret",dependencies = T). You can try this out and see if there are any dependencies other than the Biobase package for caret.
– user2730749
Nov 18 '18 at 3:47
I have had the same issue as the questioner. I attempted this and once I tried
library(caret) I got the same 1st error as the questioner.– a.powell
Nov 13 '18 at 18:25
I have had the same issue as the questioner. I attempted this and once I tried
library(caret) I got the same 1st error as the questioner.– a.powell
Nov 13 '18 at 18:25
Maybe it has something to do with the R version, as pointed out by a previous response. I was using R version 3.5.1 (2018-07-02) under Windows 10 Pro. And I used install.packages("caret",dependencies = T). You can try this out and see if there are any dependencies other than the Biobase package for caret.
– user2730749
Nov 18 '18 at 3:47
Maybe it has something to do with the R version, as pointed out by a previous response. I was using R version 3.5.1 (2018-07-02) under Windows 10 Pro. And I used install.packages("caret",dependencies = T). You can try this out and see if there are any dependencies other than the Biobase package for caret.
– user2730749
Nov 18 '18 at 3:47
add a comment |
Warning ...
install.packages("BiocManager")
This only works if your R version is >= 3.5.0
for info I've the same problem under a Centos and a Windows.
issue solved on the windows with 3.5.1 R version. Not yet solved on the centOS (3.4.2)
answered Nov 13 '18 at 10:13
G. XibG. Xib
12
add a comment |
Warning ...
install.packages("BiocManager")
This only works if your R version is >= 3.5.0
for info I've the same problem under a Centos and a Windows.
issue solved on the windows with 3.5.1 R version. Not yet solved on the centOS (3.4.2)
answered Nov 13 '18 at 10:13
G. XibG. Xib
12
add a comment |
Warning ...
install.packages("BiocManager")
This only works if your R version is >= 3.5.0
for info I've the same problem under a Centos and a Windows.
issue solved on the windows with 3.5.1 R version. Not yet solved on the centOS (3.4.2)
answered Nov 13 '18 at 10:13
G. XibG. Xib
12
Warning ...
install.packages("BiocManager")
This only works if your R version is >= 3.5.0
for info I've the same problem under a Centos and a Windows.
issue solved on the windows with 3.5.1 R version. Not yet solved on the centOS (3.4.2)
answered Nov 13 '18 at 10:13
G. XibG. Xib
12
answered Nov 13 '18 at 10:13
G. XibG. Xib
12
answered Nov 13 '18 at 10:13
G. XibG. Xib
12
answered Nov 13 '18 at 10:13
G. XibG. Xib
12
12
add a comment |
add a comment |
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1
Have you tried installing
biobasefirst? See the documentation for installation help– CIAndrews
Nov 13 '18 at 0:52
These are confusing messages. Biobase is a Bioconductor package. Neither it, nor dimRed seem to be required for caret, according to its CRAN page. It sounds like your current R environment is just messed up. I would restart R and try again.
– neilfws
Nov 13 '18 at 0:56
It's possible that one of the package required by
caret(and there are a big boatload of them) does havedimRedas a dependency. I just installedcaretand dimRed was installed during the dependencies phase. Si suggestions to reinstall my be a waste of time. (I did already have Biobase installed.)– 42-
Nov 13 '18 at 1:43
I ran install.packages("dimRed", dependencies = T) and now my base error message has changed to - > library("caret") Error: package or namespace load failed for ‘caret’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘Biobase’. When I try to install Biobase, I'm told that it is not available on R3.4.4. Any ideas?
– coult
Nov 13 '18 at 2:38