#> Error in {: task 1 failed - "object 'fun_name' not found" about cola HOT 18 CLOSED

Emmm... This is annoying 😩

Can you try the newest version from GitHub? I and my student jus tried and everything seems working fine.

There will be a new Bioconductor release next month. Hope this error will not appear any more.

Wow!!! very thanks !! the newest version work very well!!

from cola.

You need to update the ComplexHeatmap package.

library(devtools)
install_github("jokergoo/ComplexHeatmap")

from cola.

You need to update the ComplexHeatmap package.

library(devtools)
install_github("jokergoo/ComplexHeatmap")

Thank you very much , I updated the ComplexHeatmap package,but it seems not useful.
The function alone plot_ecdf() and consensus_heatmap() is useful.

from cola.

Have you restarted your R session?

from cola.

Have you restarted your R session?

Yes,I did it.However, nothing change. This is the report html.
cola_report.zip

from cola.

Can you provide me your session info?

from cola.

Can you provide me your session info?、

I'm very sorry, I'm novice to R. I don't know if this is what you're talking about.

devtools::session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.2.1 (2022-06-23 ucrt)
os Windows 10 x64 (build 19043)
system x86_64, mingw32
ui RStudio
language (EN)
collate Chinese (Simplified)_China.utf8
ctype Chinese (Simplified)_China.utf8
tz Asia/Taipei
date 2022-10-10
rstudio 2022.07.1+554 Spotted Wakerobin (desktop)
pandoc NA

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
! package * version date (UTC) lib source
abind 1.4-5 2016-07-21 [1] CRAN (R 4.2.0)
annotate 1.74.0 2022-04-28 [1] Bioconductor
AnnotationDbi 1.58.0 2022-04-26 [1] Bioconductor
ape 5.6-2 2022-03-02 [1] CRAN (R 4.2.1)
aplot 0.1.7 2022-09-06 [1] CRAN (R 4.2.1)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.2.1)
backports 1.4.1 2021-12-13 [1] CRAN (R 4.2.0)
beachmat 2.12.0 2022-04-26 [1] Bioconductor
Biobase 2.56.0 2022-04-26 [1] Bioconductor
BiocGenerics 0.42.0 2022-04-26 [1] Bioconductor
BiocManager 1.30.18 2022-05-18 [1] CRAN (R 4.2.1)
BiocParallel * 1.30.3 2022-06-07 [1] Bioconductor
BiocSingular 1.12.0 2022-04-26 [1] Bioconductor
Biostrings 2.64.1 2022-08-25 [1] Bioconductor
bit 4.0.4 2020-08-04 [1] CRAN (R 4.2.1)
bit64 4.0.5 2020-08-30 [1] CRAN (R 4.2.1)
bitops 1.0-7 2021-04-24 [1] CRAN (R 4.2.0)
blob 1.2.3 2022-04-10 [1] CRAN (R 4.2.1)
brew 1.0-7 2022-02-04 [1] CRAN (R 4.2.1)
broom 1.0.1 2022-08-29 [1] CRAN (R 4.2.1)
cachem 1.0.6 2021-08-19 [1] CRAN (R 4.2.1)
callr 3.7.2 2022-08-22 [1] CRAN (R 4.2.1)
car 3.1-0 2022-06-15 [1] CRAN (R 4.2.1)
carData 3.0-5 2022-01-06 [1] CRAN (R 4.2.1)
cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.2.1)
circlize 0.4.15 2022-05-10 [1] CRAN (R 4.2.1)
class 7.3-20 2022-01-16 [1] CRAN (R 4.2.1)
cli 3.4.0 2022-09-08 [1] CRAN (R 4.2.1)
clue 0.3-61 2022-05-30 [1] CRAN (R 4.2.1)
cluster 2.1.4 2022-08-22 [1] CRAN (R 4.2.1)
clusterProfiler * 4.4.4 2022-06-21 [1] Bioconductor
codetools 0.2-18 2020-11-04 [1] CRAN (R 4.2.1)
cola * 2.2.0 2022-04-26 [1] Bioconductor
colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.2.1)
ComplexHeatmap * 2.13.2 2022-10-10 [1] Github (jokergoo/ComplexHeatmap@cdb9fb7)
ConsensusClusterPlus * 1.60.0 2022-04-26 [1] Bioconductor
corrplot 0.92 2021-11-18 [1] CRAN (R 4.2.1)
cowplot 1.1.1 2020-12-30 [1] CRAN (R 4.2.1)
crayon 1.5.2 2022-09-29 [1] CRAN (R 4.2.1)
data.table 1.14.2 2021-09-27 [1] CRAN (R 4.2.1)
DBI 1.1.3 2022-06-18 [1] CRAN (R 4.2.1)
dbplyr 2.2.1 2022-06-27 [1] CRAN (R 4.2.1)
DelayedArray 0.22.0 2022-04-26 [1] Bioconductor
DelayedMatrixStats 1.18.0 2022-04-26 [1] Bioconductor
dendextend 1.16.0 2022-07-04 [1] CRAN (R 4.2.1)
DESeq2 1.36.0 2022-04-26 [1] Bioconductor
devtools 2.4.4 2022-07-20 [1] CRAN (R 4.2.1)
digest 0.6.29 2021-12-01 [1] CRAN (R 4.2.1)
DO.db 2.9 2022-09-14 [1] Bioconductor
doParallel 1.0.17 2022-02-07 [1] CRAN (R 4.2.1)
DOSE 3.22.1 2022-08-30 [1] Bioconductor
downloader 0.4 2015-07-09 [1] CRAN (R 4.2.1)
dplyr * 1.0.10 2022-09-01 [1] CRAN (R 4.2.1)
e1071 1.7-11 2022-06-07 [1] CRAN (R 4.2.1)
edgeR 3.38.4 2022-08-11 [1] Bioconductor
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.1)
enrichplot 1.17.2 2022-09-20 [1] Github (YuLab-SMU/enrichplot@01dfdd2)
eulerr 6.1.1 2021-09-06 [1] CRAN (R 4.2.1)
fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.1)
farver 2.1.1 2022-07-06 [1] CRAN (R 4.2.1)
fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.1)
fastmatch 1.1-3 2021-07-23 [1] CRAN (R 4.2.0)
fgsea 1.22.0 2022-04-26 [1] Bioconductor
forcats * 0.5.2 2022-08-19 [1] CRAN (R 4.2.1)
foreach 1.5.2 2022-02-02 [1] CRAN (R 4.2.1)
fs 1.5.2 2021-12-08 [1] CRAN (R 4.2.1)
gargle 1.2.1 2022-09-08 [1] CRAN (R 4.2.1)
genefilter * 1.78.0 2022-04-26 [1] Bioconductor
geneplotter 1.74.0 2022-04-26 [1] Bioconductor
generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.1)
GenomeInfoDb 1.32.4 2022-09-06 [1] Bioconductor
GenomeInfoDbData 1.2.8 2022-09-14 [1] Bioconductor
GenomicRanges 1.48.0 2022-04-26 [1] Bioconductor
GetoptLong 1.0.5 2020-12-15 [1] CRAN (R 4.2.1)
ggforce 0.3.4 2022-08-18 [1] CRAN (R 4.2.1)
ggfun 0.0.7 2022-08-31 [1] CRAN (R 4.2.1)
ggplot2 * 3.3.6 2022-05-03 [1] CRAN (R 4.2.1)
ggplotify 0.1.0 2021-09-02 [1] CRAN (R 4.2.1)
ggpubr * 0.4.0 2020-06-27 [1] CRAN (R 4.2.1)
ggraph 2.0.6 2022-08-08 [1] CRAN (R 4.2.1)
ggrepel 0.9.1 2021-01-15 [1] CRAN (R 4.2.1)
ggsignif 0.6.3 2021-09-09 [1] CRAN (R 4.2.1)
ggtree 3.4.2 2022-08-14 [1] Bioconductor
glmnet 4.1-4 2022-04-15 [1] CRAN (R 4.2.1)
GlobalOptions 0.1.2 2020-06-10 [1] CRAN (R 4.2.1)
glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.1)
GO.db 3.15.0 2022-09-14 [1] Bioconductor
googledrive 2.0.0 2021-07-08 [1] CRAN (R 4.2.1)
googlesheets4 1.0.1 2022-08-13 [1] CRAN (R 4.2.1)
GOSemSim 2.22.0 2022-04-26 [1] Bioconductor
graph 1.74.0 2022-04-26 [1] Bioconductor
graphlayouts 0.8.1 2022-08-11 [1] CRAN (R 4.2.1)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.2.1)
gridGraphics 0.5-1 2020-12-13 [1] CRAN (R 4.2.1)
GSEABase 1.58.0 2022-04-26 [1] Bioconductor
GSVA 1.44.3 2022-09-11 [1] Bioconductor
gtable 0.3.1 2022-09-01 [1] CRAN (R 4.2.1)
haven 2.5.1 2022-08-22 [1] CRAN (R 4.2.1)
HDF5Array 1.24.2 2022-08-02 [1] Bioconductor
hms 1.1.2 2022-08-19 [1] CRAN (R 4.2.1)
htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.2.1)
htmlwidgets 1.5.4 2021-09-08 [1] CRAN (R 4.2.1)
httpuv 1.6.6 2022-09-08 [1] CRAN (R 4.2.1)
httr 1.4.4 2022-08-17 [1] CRAN (R 4.2.1)
igraph 1.3.5 2022-09-22 [1] CRAN (R 4.2.1)
impute 1.70.0 2022-04-26 [1] Bioconductor
IOBR * 0.99.9 2022-09-14 [1] Github (IOBR/IOBR@de63e20)
IRanges 2.30.1 2022-08-25 [1] Bioconductor
irlba 2.3.5.1 2022-10-03 [1] CRAN (R 4.2.1)
iterators 1.0.14 2022-02-05 [1] CRAN (R 4.2.1)
jsonlite 1.8.2 2022-10-02 [1] CRAN (R 4.2.1)
KEGGREST 1.36.3 2022-07-14 [1] Bioconductor
km.ci 0.5-6 2022-04-06 [1] CRAN (R 4.2.1)
KMsurv 0.1-5 2012-12-03 [1] CRAN (R 4.2.0)
knitr 1.40 2022-08-24 [1] CRAN (R 4.2.1)
later 1.3.0 2021-08-18 [1] CRAN (R 4.2.1)
lattice 0.20-45 2021-09-22 [1] CRAN (R 4.2.1)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.2.1)
lifecycle 1.0.2 2022-09-09 [1] CRAN (R 4.2.1)
limma * 3.52.3 2022-09-11 [1] Bioconductor
limSolve 1.5.6 2019-11-14 [1] CRAN (R 4.2.1)
locfit 1.5-9.6 2022-07-11 [1] CRAN (R 4.2.1)
lpSolve 5.6.16 2022-09-04 [1] CRAN (R 4.2.1)
lubridate 1.8.0 2021-10-07 [1] CRAN (R 4.2.1)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.1)
markdown 1.1 2019-08-07 [1] CRAN (R 4.2.1)
MASS 7.3-58.1 2022-08-03 [1] CRAN (R 4.2.1)
Matrix 1.5-1 2022-09-13 [1] CRAN (R 4.2.1)
MatrixGenerics 1.8.1 2022-06-30 [1] Bioconductor
matrixStats 0.62.0 2022-04-19 [1] CRAN (R 4.2.1)
mclust 5.4.10 2022-05-20 [1] CRAN (R 4.2.1)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.2.1)
mgcv * 1.8-40 2022-03-29 [1] CRAN (R 4.2.1)
microbenchmark 1.4.9 2021-11-09 [1] CRAN (R 4.2.1)
mime 0.12 2021-09-28 [1] CRAN (R 4.2.0)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.2.1)
modelr 0.1.9 2022-08-19 [1] CRAN (R 4.2.1)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.1)
nlme * 3.1-159 2022-08-09 [1] CRAN (R 4.2.1)
org.Hs.eg.db 3.15.0 2022-09-14 [1] Bioconductor
patchwork 1.1.2 2022-08-19 [1] CRAN (R 4.2.1)
pheatmap 1.0.12 2019-01-04 [1] CRAN (R 4.2.1)
pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.1)
pkgbuild 1.3.1 2021-12-20 [1] CRAN (R 4.2.1)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.1)
pkgload 1.3.0 2022-06-27 [1] CRAN (R 4.2.1)
plyr 1.8.7 2022-03-24 [1] CRAN (R 4.2.1)
png 0.1-7 2013-12-03 [1] CRAN (R 4.2.0)
polyclip 1.10-0 2019-03-14 [1] CRAN (R 4.2.0)
preprocessCore * 1.58.0 2022-04-26 [1] Bioconductor
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.2.1)
processx 3.7.0 2022-07-07 [1] CRAN (R 4.2.1)
profvis 0.3.7 2020-11-02 [1] CRAN (R 4.2.1)
promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.2.1)
proxy 0.4-27 2022-06-09 [1] CRAN (R 4.2.1)
ps 1.7.1 2022-06-18 [1] CRAN (R 4.2.1)
purrr * 0.3.4 2020-04-17 [1] CRAN (R 4.2.1)
quadprog 1.5-8 2019-11-20 [1] CRAN (R 4.2.0)
qvalue 2.28.0 2022-04-26 [1] Bioconductor
R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.1)
RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.2.0)
Rcpp 1.0.9 2022-07-08 [1] CRAN (R 4.2.1)
RCurl 1.98-1.8 2022-07-30 [1] CRAN (R 4.2.1)
readr * 2.1.3 2022-10-01 [1] CRAN (R 4.2.1)
readxl 1.4.1 2022-08-17 [1] CRAN (R 4.2.1)
remotes 2.4.2 2021-11-30 [1] CRAN (R 4.2.1)
reprex 2.0.2 2022-08-17 [1] CRAN (R 4.2.1)
reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.2.1)
rhdf5 2.40.0 2022-04-26 [1] Bioconductor
D rhdf5filters 1.8.0 2022-04-26 [1] Bioconductor
Rhdf5lib 1.18.2 2022-05-15 [1] Bioconductor
rjson 0.2.21 2022-01-09 [1] CRAN (R 4.2.0)
rlang 1.0.5 2022-08-31 [1] CRAN (R 4.2.1)
RSQLite 2.2.17 2022-09-10 [1] CRAN (R 4.2.1)
rstatix 0.7.0 2021-02-13 [1] CRAN (R 4.2.1)
rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.1)
rsvd 1.0.5 2021-04-16 [1] CRAN (R 4.2.1)
rvest 1.0.3 2022-08-19 [1] CRAN (R 4.2.1)
S4Vectors 0.34.0 2022-04-26 [1] Bioconductor
ScaledMatrix 1.4.1 2022-09-11 [1] Bioconductor
scales 1.2.1 2022-08-20 [1] CRAN (R 4.2.1)
scatterpie 0.1.8 2022-09-03 [1] CRAN (R 4.2.1)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.1)
shadowtext 0.1.2 2022-04-22 [1] CRAN (R 4.2.1)
shape 1.4.6 2021-05-19 [1] CRAN (R 4.2.0)
shiny 1.7.2 2022-07-19 [1] CRAN (R 4.2.1)
SingleCellExperiment 1.18.0 2022-04-26 [1] Bioconductor
skmeans 0.2-14 2021-11-16 [1] CRAN (R 4.2.1)
slam 0.1-50 2022-01-08 [1] CRAN (R 4.2.0)
sparseMatrixStats 1.8.0 2022-04-26 [1] Bioconductor
stringi 1.7.8 2022-07-11 [1] CRAN (R 4.2.1)
stringr * 1.4.1 2022-08-20 [1] CRAN (R 4.2.1)
SummarizedExperiment 1.26.1 2022-04-29 [1] Bioconductor
survival * 3.4-0 2022-08-09 [1] CRAN (R 4.2.1)
survminer 0.4.9 2021-03-09 [1] CRAN (R 4.2.1)
survMisc 0.5.6 2022-04-07 [1] CRAN (R 4.2.1)
sva * 3.44.0 2022-04-26 [1] Bioconductor
tibble * 3.1.8 2022-07-22 [1] CRAN (R 4.2.1)
tidygraph 1.2.2 2022-08-22 [1] CRAN (R 4.2.1)
tidyHeatmap * 1.8.1 2022-05-20 [1] CRAN (R 4.2.1)
tidyr * 1.2.1 2022-09-08 [1] CRAN (R 4.2.1)
tidyselect 1.1.2 2022-02-21 [1] CRAN (R 4.2.1)
tidytree 0.4.0 2022-08-13 [1] CRAN (R 4.2.1)
tidyverse * 1.3.2 2022-07-18 [1] CRAN (R 4.2.1)
tinyarray * 2.2.7 2021-11-08 [1] CRAN (R 4.2.1)
treeio 1.20.2 2022-08-14 [1] Bioconductor
tweenr 2.0.2 2022-09-06 [1] CRAN (R 4.2.1)
tzdb 0.3.0 2022-03-28 [1] CRAN (R 4.2.1)
urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.2.1)
usethis 2.1.6 2022-05-25 [1] CRAN (R 4.2.1)
utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.1)
vctrs 0.4.2 2022-09-29 [1] CRAN (R 4.2.1)
viridis 0.6.2 2021-10-13 [1] CRAN (R 4.2.1)
viridisLite 0.4.1 2022-08-22 [1] CRAN (R 4.2.1)
withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.1)
xfun 0.33 2022-09-12 [1] CRAN (R 4.2.1)
XML 3.99-0.10 2022-06-09 [1] CRAN (R 4.2.1)
xml2 1.3.3 2021-11-30 [1] CRAN (R 4.2.1)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.2.1)
XVector 0.36.0 2022-04-26 [1] Bioconductor
yulab.utils 0.0.5 2022-06-30 [1] CRAN (R 4.2.1)
zlibbioc 1.42.0 2022-04-26 [1] Bioconductor
zoo 1.8-11 2022-09-17 [1] CRAN (R 4.2.1)

[1] C:/Program Files/R/R-4.2.1/library

D ── DLL MD5 mismatch, broken installation.

from cola.

Maybe. you can also update cola from GitHub:

library(devtools)
install_github("jokergoo/cola")

I just tested with the newest version of cola, it works OK.

from cola.

Maybe. you can also update cola from GitHub:

library(devtools)
install_github("jokergoo/cola")

I just tested with the newest version of cola, it works OK.

Thank you very much!

from cola.

I am also having this issue and downloading the latest ComplexHeatmap and Cola from github did not resolve it. Any other suggestions for troubleshooting?

from cola.

When you say "the latest ComplexHeatmap and Cola", what are the version numbers of these two?

from cola.

Thanks for the quick reply. I am installing using install_github() which is accessing ComplexHeatmap_2.15.1 and cola_2.3.5

Is there something else I should be specifying?

from cola.

Have you restarted your R session or the object returned by run_all_consensus_partition_methods() was still generated from the older version of cola?

from cola.

I am also having this issue, and my ComplexHeatmap and Cola are the latest versions.
My R version is 4.1.3, cola: 2.5.1; complexheatmap: 2.15.2.
Could you please give me some suggestions, thanks so much!!

from cola.

I am also having this issue, and my ComplexHeatmap and Cola are the latest versions. My R version is 4.1.3, cola: 2.5.1; complexheatmap: 2.15.2. Could you please give me some suggestions, thanks so much!!

I am using the example data (golub_cola), and it doesn;t work for [collect_plots]. However, it works well for [collect_classes]

from cola.

I am also having this issue, and my ComplexHeatmap and Cola are the latest versions. My R version is 4.1.3, cola: 2.5.1; complexheatmap: 2.15.2. Could you please give me some suggestions, thanks so much!!

I did not solved this problem, and I used collect for every K to choose the result.... and use single function get other figures.

from cola.

Emmm... This is annoying 😩

Can you try the newest version from GitHub? I and my student jus tried and everything seems working fine.

There will be a new Bioconductor release next month. Hope this error will not appear any more.

from cola.

Hi everyone, today I realized the error is from the function collect_plots() where temporary png files are generated. Currently there is a problem that 1 either some variables (e.g. fun_name) cannot be properly sent into the parallel code chunk, and 2 putting png() inside the parallel code chunk makes the execution forever. I don't know why and it needs time to fix that.

Current solution is that I replaced the old parallel code with a simple lapply(). This means there won't be any parallel execution of generating figures, but at least it is safer.

from cola.