TCGA2STAT difficulties
I am trying to get data out of the TCGA2STAT package, but cannot seem to get past this error:
RNASeqV2 data will be imported! This may take some time!
running command 'C:Rtoolsbintar -ztf "OV-RNAseq2GeneNorm.tar.gz"' had status 2
tar (child): gzip: Cannot exec: No such file or directory
tar (child): Error is not recoverable: exiting now
/Rtools/bin/tar: Child returned status 2
/Rtools/bin/tar: Error is not recoverable: exiting now
�C:Rtoolsbintar -zxf "OV-RNAseq2GeneNorm.tar.gz"� returned error code 2
Error in file.rename(from = fileList, to = fname) :
'from' and 'to' are of different lengths
Here is my code:
Sys.setenv(R_GZIPCMD ="C:\Rtools\bin\gzip")
Sys.setenv(TAR ="C:\Rtools\bin\tar")
TCGA_OV <- getTCGA(disease = "OV", data.type = "RNASeq2", clinical = T)
I have tried troubleshooting the tar path and the file.rename error but have not gotten past this point (already had to fix a few other things--R 3.5.1 doesn't seem to work well with Rtools). Thanks for your help!
r
asked Nov 10 at 2:46
user10631646
12
add a comment |
I am trying to get data out of the TCGA2STAT package, but cannot seem to get past this error:
RNASeqV2 data will be imported! This may take some time!
running command 'C:Rtoolsbintar -ztf "OV-RNAseq2GeneNorm.tar.gz"' had status 2
tar (child): gzip: Cannot exec: No such file or directory
tar (child): Error is not recoverable: exiting now
/Rtools/bin/tar: Child returned status 2
/Rtools/bin/tar: Error is not recoverable: exiting now
�C:Rtoolsbintar -zxf "OV-RNAseq2GeneNorm.tar.gz"� returned error code 2
Error in file.rename(from = fileList, to = fname) :
'from' and 'to' are of different lengths
Here is my code:
Sys.setenv(R_GZIPCMD ="C:\Rtools\bin\gzip")
Sys.setenv(TAR ="C:\Rtools\bin\tar")
TCGA_OV <- getTCGA(disease = "OV", data.type = "RNASeq2", clinical = T)
I have tried troubleshooting the tar path and the file.rename error but have not gotten past this point (already had to fix a few other things--R 3.5.1 doesn't seem to work well with Rtools). Thanks for your help!
r
asked Nov 10 at 2:46
user10631646
12
add a comment |
I am trying to get data out of the TCGA2STAT package, but cannot seem to get past this error:
RNASeqV2 data will be imported! This may take some time!
running command 'C:Rtoolsbintar -ztf "OV-RNAseq2GeneNorm.tar.gz"' had status 2
tar (child): gzip: Cannot exec: No such file or directory
tar (child): Error is not recoverable: exiting now
/Rtools/bin/tar: Child returned status 2
/Rtools/bin/tar: Error is not recoverable: exiting now
�C:Rtoolsbintar -zxf "OV-RNAseq2GeneNorm.tar.gz"� returned error code 2
Error in file.rename(from = fileList, to = fname) :
'from' and 'to' are of different lengths
Here is my code:
Sys.setenv(R_GZIPCMD ="C:\Rtools\bin\gzip")
Sys.setenv(TAR ="C:\Rtools\bin\tar")
TCGA_OV <- getTCGA(disease = "OV", data.type = "RNASeq2", clinical = T)
I have tried troubleshooting the tar path and the file.rename error but have not gotten past this point (already had to fix a few other things--R 3.5.1 doesn't seem to work well with Rtools). Thanks for your help!
r
asked Nov 10 at 2:46
user10631646
12
I am trying to get data out of the TCGA2STAT package, but cannot seem to get past this error:
RNASeqV2 data will be imported! This may take some time!
running command 'C:Rtoolsbintar -ztf "OV-RNAseq2GeneNorm.tar.gz"' had status 2
tar (child): gzip: Cannot exec: No such file or directory
tar (child): Error is not recoverable: exiting now
/Rtools/bin/tar: Child returned status 2
/Rtools/bin/tar: Error is not recoverable: exiting now
�C:Rtoolsbintar -zxf "OV-RNAseq2GeneNorm.tar.gz"� returned error code 2
Error in file.rename(from = fileList, to = fname) :
'from' and 'to' are of different lengths
Here is my code:
Sys.setenv(R_GZIPCMD ="C:\Rtools\bin\gzip")
Sys.setenv(TAR ="C:\Rtools\bin\tar")
TCGA_OV <- getTCGA(disease = "OV", data.type = "RNASeq2", clinical = T)
I have tried troubleshooting the tar path and the file.rename error but have not gotten past this point (already had to fix a few other things--R 3.5.1 doesn't seem to work well with Rtools). Thanks for your help!
r
r
asked Nov 10 at 2:46
user10631646
12
asked Nov 10 at 2:46
user10631646
12
edited Nov 10 at 3:15
asked Nov 10 at 2:46
user10631646
12
asked Nov 10 at 2:46
user10631646
12
asked Nov 10 at 2:46
user10631646
12
12
add a comment |
add a comment |
active
oldest
votes
Your Answer
StackExchange.ifUsing("editor", function ()
StackExchange.using("externalEditor", function ()
StackExchange.using("snippets", function ()
StackExchange.snippets.init();
);
);
, "code-snippets");
StackExchange.ready(function()
var channelOptions =
tags: "".split(" "),
id: "1"
;
initTagRenderer("".split(" "), "".split(" "), channelOptions);
StackExchange.using("externalEditor", function()
// Have to fire editor after snippets, if snippets enabled
if (StackExchange.settings.snippets.snippetsEnabled)
StackExchange.using("snippets", function()
createEditor();
);
else
createEditor();
);
function createEditor()
StackExchange.prepareEditor(
heartbeatType: 'answer',
autoActivateHeartbeat: false,
convertImagesToLinks: true,
noModals: true,
showLowRepImageUploadWarning: true,
reputationToPostImages: 10,
bindNavPrevention: true,
postfix: "",
imageUploader:
brandingHtml: "Powered by u003ca class="icon-imgur-white" href="https://imgur.com/"u003eu003c/au003e",
contentPolicyHtml: "User contributions licensed under u003ca href="https://creativecommons.org/licenses/by-sa/3.0/"u003ecc by-sa 3.0 with attribution requiredu003c/au003e u003ca href="https://stackoverflow.com/legal/content-policy"u003e(content policy)u003c/au003e",
allowUrls: true
,
onDemand: true,
discardSelector: ".discard-answer"
,immediatelyShowMarkdownHelp:true
);
);
Sign up or log in
StackExchange.ready(function ()
StackExchange.helpers.onClickDraftSave('#login-link');
);
Sign up using Google
Sign up using Facebook
Sign up using Email and Password
Post as a guest
Required, but never shown
StackExchange.ready(
function ()
StackExchange.openid.initPostLogin('.new-post-login', 'https%3a%2f%2fstackoverflow.com%2fquestions%2f53235602%2ftcga2stat-difficulties%23new-answer', 'question_page');
);
Post as a guest
Required, but never shown
active
oldest
votes
active
oldest
votes
active
oldest
votes
active
oldest
votes
Thanks for contributing an answer to Stack Overflow!
- Please be sure to answer the question. Provide details and share your research!
But avoid …
- Asking for help, clarification, or responding to other answers.
- Making statements based on opinion; back them up with references or personal experience.
To learn more, see our tips on writing great answers.
Some of your past answers have not been well-received, and you're in danger of being blocked from answering.
Please pay close attention to the following guidance:
- Please be sure to answer the question. Provide details and share your research!
But avoid …
- Asking for help, clarification, or responding to other answers.
- Making statements based on opinion; back them up with references or personal experience.
To learn more, see our tips on writing great answers.
Sign up or log in
StackExchange.ready(function ()
StackExchange.helpers.onClickDraftSave('#login-link');
);
Sign up using Google
Sign up using Facebook
Sign up using Email and Password
Post as a guest
Required, but never shown
StackExchange.ready(
function ()
StackExchange.openid.initPostLogin('.new-post-login', 'https%3a%2f%2fstackoverflow.com%2fquestions%2f53235602%2ftcga2stat-difficulties%23new-answer', 'question_page');
);
Post as a guest
Required, but never shown
Sign up or log in
StackExchange.ready(function ()
StackExchange.helpers.onClickDraftSave('#login-link');
);
Sign up using Google
Sign up using Facebook
Sign up using Email and Password
Post as a guest
Required, but never shown
Sign up or log in
StackExchange.ready(function ()
StackExchange.helpers.onClickDraftSave('#login-link');
);
Sign up using Google
Sign up using Facebook
Sign up using Email and Password
Post as a guest
Required, but never shown
Sign up or log in
StackExchange.ready(function ()
StackExchange.helpers.onClickDraftSave('#login-link');
);
Sign up using Google
Sign up using Facebook
Sign up using Email and Password
Sign up using Google
Sign up using Facebook
Sign up using Email and Password
Post as a guest
Required, but never shown
Required, but never shown
Required, but never shown
Required, but never shown
Required, but never shown
Required, but never shown
Required, but never shown
Required, but never shown
Required, but never shown
