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StoreyLab / qvalue

R package to estimate q-values and false discovery rate quantities.
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function "qvalue_truncp" has been removed? #21

Closed jrager closed 4 years ago

jrager commented 4 years ago

We have been running the qvalue package smoothly, and have in some instances incorporated the function "qvalue_truncp" to deal with the issue, as explained in (among others): https://github.com/StoreyLab/qvalue/issues/11

However, recently R is throwing me the error, "Error in qvalue_truncp() could not find function "qvalue_truncp"

I tried re-installing the qvalue package, which didn't help. Where did this function go?

ajbass commented 4 years ago

It's still there. Did you install qvalue from github?

library(devtools)
install_github("StoreyLab/qvalue")

library(qvalue)
qout <- qvalue_truncp(runif(100, max=0.9))
jrager commented 4 years ago

Yes – I just ran the lines of coded provided below and received: library(qvalue) qout <- qvalue_truncp(runif(100, max=0.9)) Error in qvalue_truncp(runif(100, max = 0.9)) : could not find function "qvalue_truncp"

Thank you for the feedback!!

jrager commented 4 years ago

Sorry I didn’t mean to close this thread – was just trying to edit my comment that still remains and issue below:

Yes – I just ran the lines of coded provided below and received:

library(qvalue) qout <- qvalue_truncp(runif(100, max=0.9)) Error in qvalue_truncp(runif(100, max = 0.9)) : could not find function "qvalue_truncp"

Thank you for the feedback!!

From: Andrew Bass notifications@github.com Reply-To: StoreyLab/qvalue reply@reply.github.com Date: Saturday, January 4, 2020 at 8:25 AM To: StoreyLab/qvalue qvalue@noreply.github.com Cc: "Rager, Julia" jrager@unc.edu, Author author@noreply.github.com Subject: Re: [StoreyLab/qvalue] function "qvalue_truncp" has been removed? (#21)

It's still there. Did you install qvalue from github?

library(devtools)

install_github("StoreyLab/qvalue")

library(qvalue)

qout <- qvalue_truncp(runif(100, max=0.9))

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/StoreyLab/qvalue/issues/21?email_source=notifications&email_token=AOF2DDL5NZ6WG3RZH6QMZULQ4CE3VA5CNFSM4KCPQTI2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEICX6FQ#issuecomment-570785558, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AOF2DDJLZSWYHALZ7R47NTTQ4CE3VANCNFSM4KCPQTIQ.

ajbass commented 4 years ago

Can you send over:

library(qvalue)
library(devtools)
sessionInfo()

You should see version qvalue 2.15.0.

jrager commented 4 years ago

Yep, I see: other attached packages: [1] devtools_2.2.1 usethis_1.5.1 qvalue_2.15.0 reshape2_1.4.3 dplyr_0.8.3 ggplot2_3.2.1 data.table_1.12.8

I also tried installing it using install_github("jdstorey/qvalue"), but got the same result. I had a student run the lines that you provided on a separate computer, and it worked for him, so it is something that's happening on my computer. Let me know if anything comes to mind, but if not, I'll just have the code run on a separate computer. Thanks!