Installation Issue

[HollyRuess]

I've tried to install BioMethyl but I keep getting failures

First I git clone https://github.com/yuewangpanda/BioMethyl.git

and I tried downloading as a zip

In R (3.5.1 or 3.6), I tried install.packages("/work/BICF/s185797/programs/BioMethyl/BioMethyl/BioMethyl_1.1.tar.gz", repos = NULL)

Installing package into ?/home2/s123456/R/x86_64-pc-linux-gnu-library/3.5? (as ?lib? is unspecified) Error in untar2(tarfile, files, list, exdir, restore_times) : incomplete block on file Warning in install.packages : installation of package ?/work/BICF/s185797/programs/BioMethyl/BioMethyl/BioMethyl_1.1.tar.gz? had non-zero exit status

[parcbioinfo]

Same issue: Error in untar2(tarfile, files, list, exdir, restore_times) : incomplete block on file Can't install it.

[yuewangpanda]

Can you guys provide more information about your R version and your machine?

[parcbioinfo]

I have tried it in two environments: 1: R version 3.6.0 (2019-04-26) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

2: R version 3.5.2 (2018-12-20) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux

[HollyRuess]

R version 3.5.1 or 3.6.1 in Red Hat Enterprise Linux

[yuewangpanda]

Hey, guys. I don't know what happened to the Github large file storage. The old file was damaged. I re-uploaded the package. Now it should work for you.

git clone https://github.com/yuewangpanda/BioMethyl.git BioMethyl

install.packages("BioMethyl/BioMethyl_1.1.tar.gz", repos = NULL)

• installing source package ‘BioMethyl’ ... ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded
• DONE (BioMethyl)

[HollyRuess]

I tried again, and still get the error.

I used $ git clone https://github.com/yuewangpanda/BioMethyl.git

The file when downloaded either through cloning or as zip is incredibly small.

-rw-r--r--. 1 s123456 Core 114 Nov 14 15:16 .gitattributes -rw-r--r--. 1 s123456 Core 134 Nov 14 15:16 BioMethyl_1.0.tar.gz -rw-r--r--. 1 s123456 Core 134 Nov 14 15:16 BioMethyl_1.1.tar.gz drwxr-xr-x. 2 s123456 Core 4096 Nov 14 15:16 R drwxr-xr-x. 4 s123456 Core 4096 Nov 14 15:16 . -rw-r--r--. 1 s123456 Core 4544 Nov 14 15:16 README.md drwxr-xr-x. 8 s123456 Core 4096 Nov 14 15:16 .git drwxr-xr-x. 4 s123456 Core 4096 Nov 14 15:18 ..

[yuewangpanda]

I cannot repeat your error. I just re-did this and it works well to me. Here is my code.

git clone https://github.com/yuewangpanda/BioMethyl.git BioMethyl2 install.packages("BioMethyl2/BioMethyl_1.1.tar.gz", repos = NULL)

• installing source package ‘BioMethyl’ ... ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded
• DONE (BioMethyl)

Maybe you can try to clone into a new folder? If it still can not work, I can share the package with you by dropbox. Let me know your email.

On Thu, Nov 14, 2019 at 4:26 PM Holly Ruess [email protected] wrote:

I tried again, and still get the error.

I used $ git clone https://github.com/yuewangpanda/BioMethyl.git

The file when downloaded either through cloning or as zip is incredibly small.

-rw-r--r--. 1 s123456 Core 114 Nov 14 15:16 .gitattributes -rw-r--r--. 1 s123456 Core 134 Nov 14 15:16 BioMethyl_1.0.tar.gz -rw-r--r--. 1 s123456 Core 134 Nov 14 15:16 BioMethyl_1.1.tar.gz drwxr-xr-x. 2 s123456 Core 4096 Nov 14 15:16 R drwxr-xr-x. 4 s123456 Core 4096 Nov 14 15:16 . -rw-r--r--. 1 s123456 Core 4544 Nov 14 15:16 README.md drwxr-xr-x. 8 s123456 Core 4096 Nov 14 15:16 .git drwxr-xr-x. 4 s123456 Core 4096 Nov 14 15:18 ..

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[parcbioinfo]

Doesn't work for me either: install.packages("./BioMethyl2/BioMethyl_1.1.tar.gz", repos=NULL) Installing package into ‘R/x86_64-redhat-linux-gnu-library/3.6’ (as ‘lib’ is unspecified) Error in untar2(tarfile, files, list, exdir, restore_times) : incomplete block on file Warning in install.packages : installation of package ‘BioMethyl2/BioMethyl_1.1.tar.gz’ had non-zero exit status

[yuewangpanda]

Can you provide your email to me? I am going to share it through dropbox.

[parcbioinfo]

[email protected]

[yuewangpanda]

shared. Please copy it out.

On Tue, Nov 19, 2019 at 3:56 PM P Darakjian [email protected] wrote:

Yes. [email protected]mailto:[email protected] Thanks!

From: Yue Wang [email protected] Sent: Tuesday, November 19, 2019 12:55 PM To: yuewangpanda/BioMethyl [email protected] Cc: Priscila Darakjian [email protected]; Comment < [email protected]> Subject: Re: [yuewangpanda/BioMethyl] Installation Issue (#2)

Can you provide your email to me? I am going to share it through dropbox.

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[mmorselli17]

Hi all, did it work? I have the same issues here. Can you please share it with me, too?

[yuewangpanda]

Sorry about the inconvenience. Please leave your email address.

Thanks, Frank

On Fri, Dec 6, 2019 at 7:24 AM mmorselli17 [email protected] wrote:

Hi all, did it work? I have the same issues here. Can you please share it with me, too?

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[mmorselli17]

No worries. Here is my email address: [email protected]

Thanks,

Marco.

Sent from my iPhone.

On Dec 6, 2019, at 6:23 AM, Yue Wang [email protected] wrote:

Sorry about the inconvenience. Please leave your email address.

Thanks, Frank

On Fri, Dec 6, 2019 at 7:24 AM mmorselli17 [email protected] wrote:

Hi all, did it work? I have the same issues here. Can you please share it with me, too?

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[yuewangpanda]

Just did. Please copy it out.

Thanks, Frank

On Fri, Dec 6, 2019 at 10:01 AM mmorselli17 [email protected] wrote:

No worries. Here is my email address: [email protected]

Thanks,

Marco.

Sent from my iPhone.

On Dec 6, 2019, at 6:23 AM, Yue Wang [email protected] wrote:

Sorry about the inconvenience. Please leave your email address.

Thanks, Frank

On Fri, Dec 6, 2019 at 7:24 AM mmorselli17 [email protected] wrote:

Hi all, did it work? I have the same issues here. Can you please share it with me, too?

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[mmorselli17]

Thanks a lot!!

Marco.

On Fri, Dec 6, 2019 at 7:27 AM Yue Wang [email protected] wrote:

Just did. Please copy it out.

Thanks, Frank

On Fri, Dec 6, 2019 at 10:01 AM mmorselli17 [email protected] wrote:

No worries. Here is my email address: [email protected]

Thanks,

Marco.

Sent from my iPhone.

On Dec 6, 2019, at 6:23 AM, Yue Wang [email protected] wrote:

Sorry about the inconvenience. Please leave your email address.

Thanks, Frank

On Fri, Dec 6, 2019 at 7:24 AM mmorselli17 [email protected] wrote:

Hi all, did it work? I have the same issues here. Can you please share it with me, too?

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,

or unsubscribe <

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-- Best,

Marco.

[Ekrates]

Dear all,

the installation doesn't really seem to work, same issues as above. Here's my email (at = @): ejvest at utu.fi

Best, Eero

[yuewangpanda]

Sorry for the late reply and inconvenience. Please copy the package to your local environment.

Best, Frank

On Sat, Dec 14, 2019 at 1:31 PM Ekrates [email protected] wrote:

Dear all,

the installation doesn't really seem to work, same issues as above. Here's my email (at = @): ejvest at utu.fi

Best, Eero

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[Jeong-RyeolGong]

Dear yuewangpanda I have same problems to install the packages Can you send me source code? My email is "***" Thank you

best

Jeong-Ryeol

[yuewangpanda]

Please copy the package out.

Thanks, Frank

On Fri, Jan 3, 2020 at 12:58 AM Jeong-RyeolGong [email protected] wrote:

Dear yuewangpanda I have same problems to install the packages Can you send me source code? My email is "[email protected]" Thank you

best

Jeong-Ryeol

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[yuewangpanda]

Hi all,

If you fail to install the package from Github, please download it from my personal webpage (https://morgan1.dartmouth.edu/~f002nfh/BioMethyl/) or send me your email address if you have a dropbox account. Sorry for the inconvenience.

Trying to fix the problem. If you happen to know how to keep the file using the large-file storage (LFS) uploading approach active, please let me know. Any help will be appreciated.

Thank you for having interests in the BioMethyl package.

Frank

[yangjunhuicq]

Dear yuewangpanda,

I have same problems to install the packages. Would you please send me source code? My email is [email protected].

Thank you very much!

Best regards!

Junhui

[yuewangpanda]

Hi Junhui,

Just shared the source package with you through dropbox. Let me know if you still have issues.

Best, Frank

On Mon, Aug 10, 2020 at 4:29 AM yangjunhuicq [email protected] wrote:

Dear yuewangpanda,

I have same problems to install the packages. Would you please send me source code? My email is [email protected].

Thank you very much!

Best regards!

Junhui

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[yangjunhuicq]

Hi, Frank

Thanks for your quick response. Since I'm new to Github and dropbox, I don't know how I can get the source package you shared with me.

Junhui

Hi Junhui, Just shared the source package with you through dropbox. Let me know if you still have issues. Best, Frank …

[yuewangpanda]

Hi Junhui,

Do you have a dropbox account using the email address you gave me? If so, you can log into your dropbox and find the package. Please copy it out to your working directory.

Frank

On Mon, Aug 10, 2020 at 9:03 PM yangjunhuicq [email protected] wrote:

Hi, Frank

Thanks for your quick response. Since I'm new to Github and dropbox, I don't know how I can get the source package you shared with me.

Junhui

Hi Junhui, Just shared the source package with you through dropbox. Let me know if you still have issues. Best, Frank … <#m_4367958107075049595_m_7463563970141388184_>

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[yangjunhuicq]

Hi, Frank

Sorry, I don't have a dropbox account (I even cannot access to http://www.dropbox.com/). Could you send me the package by email?

Junhui

Hi Junhui, Do you have a dropbox account using the email address you gave me? If so, you can log into your dropbox and find the package. Please copy it out to your working directory. Frank

[yuewangpanda]

Hi Junhui,

Sorry to hear that. Are you in China now? The package is too big to be sent by email. If you are clear about what you are going to do, you can use the functions in the R folder following the instructions.

Frank

On Tue, Aug 11, 2020 at 8:56 PM yangjunhuicq [email protected] wrote:

Hi, Frank

Sorry, I don't hava a dropbox account (I even cannot access to http://www.dropbox.com/). Could you send me the package by email?

Junhui

Hi Junhui, Do you have a dropbox account using the email address you gave me? If so, you can log into your dropbox and find the package. Please copy it out to your working directory. Frank

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[yangjunhuicq]

Hi, Frank

Sorry for the late reply. I registered a dropbox account using my email address and successfully got the source package you shared to me. Thank you so much!

Junhui

Hi Junhui, Sorry to hear that. Are you in China now? The package is too big to be sent by email. If you are clear about what you are going to do, you can use the functions in the R folder following the instructions. Frank …

[yuewangpanda]

Just did. Let me know if you have more questions.

Frank

On Thu, Aug 13, 2020 at 8:42 PM yangjunhuicq [email protected] wrote:

Hi, Frank

Sorry for late reply. I registered a dropbox account using the email [email protected]. Would please share me the source package again? Thank you so much!

Junhui

Hi Junhui, Sorry to hear that. Are you in China now? The package is too big to be sent by email. If you are clear about what you are going to do, you can use the functions in the R folder following the instructions. Frank … <#m_5731001207276248256_>

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[dadielle]

Dear yuewangpanda,

I have the same problem to install the package. Could you please send me source code? My email is [email protected].

Thank you in addivance

Best regards Danielle Bruno