Error in if (isSparseMatrix(counts)) { : the condition has length > 1 Calls: subMonocle2 ... estimateSizeFactors -> .local -> estimateSizeFactorsForMatrix about monocle-release

[Joleen457]

Have you solved it? I have the same problem. T T

[weihuaguo]

Nope. But when I downgrade the monocle 2 into 2.18.0, the bug disappears.

[unlsysbioywl]

I also have the same problem:

cds <- estimateSizeFactors(cds)
Error in if (isSparseMatrix(counts) >= 1) { :
the condition has length > 1

Then I did the following steps and finally sovled it.

step1: download the sorce code package from https://www.bioconductor.org/packages/3.15/bioc/src/contrib/Archive/monocle/

step2: decompress the compressed package

step3: type ".libPaths()" in R console to check where the library are

.libPaths()
[1] "D:/Program Files/R/R-4.2.2/library"

step4: goto this director and find a directory of the same name "monocle"

step5: replace this directory with the one you just decompressed

step6: reload the sorce code package (maybe you need to install "devtools" first)
devtools::load_all("D:/Program Files/R/R-4.2.2/library/monocle")

step7: re-run "estimateSizeFactor(cds)"; it will return the error message and also "Return with Debug" button

step8: click "Return with Debug" button. It will show you at which line in which R script, the error comes from. Or, to be simple, you need to edit utils.R and expr_models.R

step9: edit utils.R
at line 35: chnage "isSparseMatrix(cellData)" into "isSparseMatrix(cellData)[1]"
at line 192: change "isSparseMatrix(exprs(X))" into "isSparseMatrix(exprs(X))[1]"
at line 438: change "isSparseMatrix(counts)" into "isSparseMatrix(counts)[1]"

all in all, it is because isSparseMatrix() should return one logical value-TRUE/FALSE but now it return two logical values and both them are FALSE
!!!remember to save the changes

step10: edit expr_modles.R
at line 454: change "isSparseMatrix(exprs(cds))" into "isSparseMatrix(exprs(cds))[1]"
!!!remember to save the change

step11: reload monocle
devtools::load_all("D:/Program Files/R/R-4.2.2/library/monocle")

Now, the problem is sovled

cds <- estimateSizeFactors(cds)
cds <- estimateDispersions(cds)
Removing 159 outliers

[weihuaguo]

I also have the same problem:

cds <- estimateSizeFactors(cds) Error in if (isSparseMatrix(counts) >= 1) { : the condition has length > 1

Then I did the following steps and finally sovled it.

step1: download the sorce code package from https://www.bioconductor.org/packages/3.15/bioc/src/contrib/Archive/monocle/

step2: decompress the compressed package

step3: type ".libPaths()" in R console to check where the library are

.libPaths() [1] "D:/Program Files/R/R-4.2.2/library"

step4: goto this director and find a directory of the same name "monocle"

step5: replace this directory with the one you just decompressed

step6: reload the sorce code package (maybe you need to install "devtools" first) devtools::load_all("D:/Program Files/R/R-4.2.2/library/monocle")

step7: re-run "estimateSizeFactor(cds)"; it will return the error message and also "Return with Debug" button

step8: click "Return with Debug" button. It will show you at which line in which R script, the error comes from. Or, to be simple, you need to edit utils.R and expr_models.R

step9: edit utils.R at line 35: chnage "isSparseMatrix(cellData)" into "isSparseMatrix(cellData)[1]" at line 192: change "isSparseMatrix(exprs(X))" into "isSparseMatrix(exprs(X))[1]" at line 438: change "isSparseMatrix(counts)" into "isSparseMatrix(counts)[1]" all in all, it is because the return of isSparseMatrix() shoulde return one logical value-TRUE/FALSE but now it return two logical values and both them are FALSE !!!remember to save the changes

step10: edit expr_modles.R at line 454: change "isSparseMatrix(exprs(cds))" into "isSparseMatrix(exprs(cds))[1]" !!!remember to save the change

step11: reload monocle devtools::load_all("D:/Program Files/R/R-4.2.2/library/monocle")

Now, the problem is sovled

cds <- estimateSizeFactors(cds) cds <- estimateDispersions(cds) Removing 159 outliers

Thanks, @unlsysbioywl ! Hope the cole trapnell lab can change their source codes very soon instead of we change the source codes locally...

[renqinzhan]

I also have the same problem:

cds <- estimateSizeFactors(cds) Error in if (isSparseMatrix(counts) >= 1) { : the condition has length > 1

Then I did the following steps and finally sovled it.

step1: download the sorce code package from https://www.bioconductor.org/packages/3.15/bioc/src/contrib/Archive/monocle/

step2: decompress the compressed package

step3: type ".libPaths()" in R console to check where the library are

.libPaths() [1] "D:/Program Files/R/R-4.2.2/library"

step4: goto this director and find a directory of the same name "monocle"

step5: replace this directory with the one you just decompressed

step6: reload the sorce code package (maybe you need to install "devtools" first) devtools::load_all("D:/Program Files/R/R-4.2.2/library/monocle")

step7: re-run "estimateSizeFactor(cds)"; it will return the error message and also "Return with Debug" button

step8: click "Return with Debug" button. It will show you at which line in which R script, the error comes from. Or, to be simple, you need to edit utils.R and expr_models.R

step9: edit utils.R at line 35: chnage "isSparseMatrix(cellData)" into "isSparseMatrix(cellData)[1]" at line 192: change "isSparseMatrix(exprs(X))" into "isSparseMatrix(exprs(X))[1]" at line 438: change "isSparseMatrix(counts)" into "isSparseMatrix(counts)[1]"

all in all, it is because isSparseMatrix() should return one logical value-TRUE/FALSE but now it return two logical values and both them are FALSE !!!remember to save the changes

step10: edit expr_modles.R at line 454: change "isSparseMatrix(exprs(cds))" into "isSparseMatrix(exprs(cds))[1]" !!!remember to save the change

step11: reload monocle devtools::load_all("D:/Program Files/R/R-4.2.2/library/monocle")

Now, the problem is sovled

cds <- estimateSizeFactors(cds) cds <- estimateDispersions(cds) Removing 159 outliers

Thanks, @unlsysbioywl ! Why did I get this error when I did step 11

[unlsysbioywl]

Did you follow the instructions step by step? It is very clear that there is an error at line 35 of file utils.R. Maybe you miss a "=", there should be "==". Show me the line34-36. Let me have a look at what was wrong with those lines.

…

________________________________ From: renqinzhan ***@***.***> Sent: Wednesday, April 19, 2023 10:24 AM To: cole-trapnell-lab/monocle-release ***@***.***> Cc: Weilong Yang ***@***.***>; Mention ***@***.***> Subject: Re: [cole-trapnell-lab/monocle-release] Error in if (isSparseMatrix(counts)) { : the condition has length > 1 Calls: subMonocle2 ... estimateSizeFactors -> .local -> estimateSizeFactorsForMatrix (Issue #486) Non-NU Email

________________________________ I also have the same problem: cds <- estimateSizeFactors(cds) Error in if (isSparseMatrix(counts) >= 1) { : the condition has length > 1 Then I did the following steps and finally sovled it. step1: download the sorce code package from https://www.bioconductor.org/packages/3.15/bioc/src/contrib/Archive/monocle/<https://urldefense.com/v3/__https://www.bioconductor.org/packages/3.15/bioc/src/contrib/Archive/monocle/__;!!PvXuogZ4sRB2p-tU!D_MTNdjRLnlPIhfSyYQJClK7wOB1fGVBOd40nSzXwJDnk_-LO-Bpl6oRoxmL7PMrrguqUeMaYsofKuF9V2isA63MNtC1pU3e1w$> step2: decompress the compressed package step3: type ".libPaths()" in R console to check where the library are .libPaths() [1] "D:/Program Files/R/R-4.2.2/library" step4: goto this director and find a directory of the same name "monocle" [image] <https://urldefense.com/v3/__https://user-images.githubusercontent.com/73863477/218940378-387108e1-17e2-4496-b93c-c79d3ebdc13f.png__;!!PvXuogZ4sRB2p-tU!D_MTNdjRLnlPIhfSyYQJClK7wOB1fGVBOd40nSzXwJDnk_-LO-Bpl6oRoxmL7PMrrguqUeMaYsofKuF9V2isA63MNtCX7rJ4ig$> step5: replace this directory with the one you just decompressed step6: reload the sorce code package (maybe you need to install "devtools" first) devtools::load_all("D:/Program Files/R/R-4.2.2/library/monocle") step7: re-run "estimateSizeFactor(cds)"; it will return the error message and also "Return with Debug" button [image] <https://urldefense.com/v3/__https://user-images.githubusercontent.com/73863477/218940407-395a71f5-06ef-4405-ad2d-04f44c810d4f.png__;!!PvXuogZ4sRB2p-tU!D_MTNdjRLnlPIhfSyYQJClK7wOB1fGVBOd40nSzXwJDnk_-LO-Bpl6oRoxmL7PMrrguqUeMaYsofKuF9V2isA63MNtAMa5CuWA$> step8: click "Return with Debug" button. It will show you at which line in which R script, the error comes from. Or, to be simple, you need to edit utils.R and expr_models.R step9: edit utils.R at line 35: chnage "isSparseMatrix(cellData)" into "isSparseMatrix(cellData)[1]" at line 192: change "isSparseMatrix(exprs(X))" into "isSparseMatrix(exprs(X))[1]" at line 438: change "isSparseMatrix(counts)" into "isSparseMatrix(counts)[1]" all in all, it is because isSparseMatrix() should return one logical value-TRUE/FALSE but now it return two logical values and both them are FALSE !!!remember to save the changes step10: edit expr_modles.R at line 454: change "isSparseMatrix(exprs(cds))" into "isSparseMatrix(exprs(cds))[1]" !!!remember to save the change step11: reload monocle devtools::load_all("D:/Program Files/R/R-4.2.2/library/monocle") Now, the problem is sovled cds <- estimateSizeFactors(cds) cds <- estimateDispersions(cds) Removing 159 outliers Thanks, @unlsysbioywl<https://urldefense.com/v3/__https://github.com/unlsysbioywl__;!!PvXuogZ4sRB2p-tU!D_MTNdjRLnlPIhfSyYQJClK7wOB1fGVBOd40nSzXwJDnk_-LO-Bpl6oRoxmL7PMrrguqUeMaYsofKuF9V2isA63MNtCrLUyS9g$> ! Why did I get this error when I did step 11 [image]<https://urldefense.com/v3/__https://user-images.githubusercontent.com/131277041/233123614-6081106a-99cf-4e38-9f53-0b38731aedb4.png__;!!PvXuogZ4sRB2p-tU!D_MTNdjRLnlPIhfSyYQJClK7wOB1fGVBOd40nSzXwJDnk_-LO-Bpl6oRoxmL7PMrrguqUeMaYsofKuF9V2isA63MNtBDSwdBcg$> — Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https://github.com/cole-trapnell-lab/monocle-release/issues/486*issuecomment-1514931358__;Iw!!PvXuogZ4sRB2p-tU!D_MTNdjRLnlPIhfSyYQJClK7wOB1fGVBOd40nSzXwJDnk_-LO-Bpl6oRoxmL7PMrrguqUeMaYsofKuF9V2isA63MNtC5HBx8AA$>, or unsubscribe<https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ARTRCNNRQQOGZEO77EILW4DXB77RLANCNFSM6AAAAAAUEN66XY__;!!PvXuogZ4sRB2p-tU!D_MTNdjRLnlPIhfSyYQJClK7wOB1fGVBOd40nSzXwJDnk_-LO-Bpl6oRoxmL7PMrrguqUeMaYsofKuF9V2isA63MNtDtIqZ4dw$>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[qinqqqq]

@unlsysbioywl
step1: download the sorce code package from https://www.bioconductor.org/packages/3.15/bioc/src/contrib/Archive/monocle/
Sorry,the url is unavailable . Can you offer other ways to solve the problem?