Closed a-bio90 closed 1 year ago
SamDeMario-lab
commented
1 year ago Hello! There's 2 things that are immediately coming to mind.
The first is that it might be an R version issue. Can you run:
version
and send the output? I'm thinking that those packages might not be available for your version of R.
The second is that BioManager might not be installed. I would run:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")
and the try installing again.
KevinXu264
commented
1 year ago Hey @a-bio90 adding on to the suggestion here. I think the build error could be a result of the R environment not being able to find the dependencies listed, namely ‘BiocGenerics’, ‘Rsamtools’, ‘DESeq2’, ‘GenomicAlignments’, ‘GenomicRanges’, ‘Rsubread’
Did you install these dependencies using Bioconductor already? Samtools, as you mentioned was working in your post, is only one of the many dependencies required for NanoBlot to run. If you havent installed these packages, you can either install them individually in R or install the conda environment using the provided .yml file, making sure that the conda environment is included in the R environment path.
a-bio90
commented
1 year ago Thank for you quick answers! This is the R version I have:
> version
_
platform x86_64-apple-darwin20
arch x86_64
os darwin20
system x86_64, darwin20
status
major 4
minor 3.1
year 2023
month 06
day 16
svn rev 84548
language R
version.string R version 4.3.1 (2023-06-16)
nickname Beagle Scouts I have also run if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")
But still, running the command devtools::install(build_vignettes = TRUE) I still get the same error (packages not found).
Regarding the conda environment I run these commands to set the folder containing the NanoBlot environment set by using your .yml file
old_path <- Sys.getenv("PATH")
Sys.setenv(PATH = paste(old_path, "/Users/bernarda/anaconda3/envs/nanoblotenv", sep = ":"))
If I run conda env list in my terminal the nanoblot environment is listed:
# conda environments:
#
base /Users/bernarda/anaconda3
nanoblotenv * /Users/bernarda/anaconda3/envs/nanoblotenv
/Users/bernarda/opt/anaconda3/envs/deepblink
/Users/bernarda/opt/anaconda3/envs/fq-segmentationAlso, if I run conda list after having activated the NanoBlot environment I get the following packages list:
# packages in environment at /Users/bernarda/anaconda3/envs/nanoblotenv:
#
# Name Version Build Channel
_r-mutex 1.0.1 anacondar_1 conda-forge
bedtools 2.30.0 h0e31d98_3 bioconda
bioconductor-annotate 1.72.0 r41hdfd78af_0 bioconda
bioconductor-annotationdbi 1.56.2 r41hdfd78af_0 bioconda
bioconductor-apeglm 1.16.0 r41hb890f52_2 bioconda
bioconductor-biobase 2.54.0 r41h3be46a4_2 bioconda
bioconductor-biocgenerics 0.40.0 r41hdfd78af_0 bioconda
bioconductor-biocio 1.4.0 r41hdfd78af_0 bioconda
bioconductor-biocparallel 1.28.3 r41hb890f52_1 bioconda
bioconductor-biostrings 2.62.0 r41h3be46a4_2 bioconda
bioconductor-delayedarray 0.20.0 r41h3be46a4_2 bioconda
bioconductor-deseq2 1.34.0 r41hb890f52_3 bioconda
bioconductor-genefilter 1.76.0 r41h238a2e4_2 bioconda
bioconductor-geneplotter 1.72.0 r41hdfd78af_0 bioconda
bioconductor-genomeinfodb 1.30.1 r41hdfd78af_0 bioconda
bioconductor-genomeinfodbdata 1.2.7 r41hdfd78af_2 bioconda
bioconductor-genomicalignments 1.30.0 r41h3be46a4_2 bioconda
bioconductor-genomicranges 1.46.1 r41h3be46a4_1 bioconda
bioconductor-iranges 2.28.0 r41h3be46a4_2 bioconda
bioconductor-keggrest 1.34.0 r41hdfd78af_0 bioconda
bioconductor-matrixgenerics 1.6.0 r41hdfd78af_0 bioconda
bioconductor-rhtslib 1.26.0 r41h3be46a4_2 bioconda
bioconductor-rsamtools 2.10.0 r41hb890f52_2 bioconda
bioconductor-rsubread 2.8.1 r41haba8685_0 bioconda
bioconductor-rtracklayer 1.54.0 r41h68a2ddb_0 bioconda
bioconductor-s4vectors 0.32.4 r41h3be46a4_0 bioconda
bioconductor-summarizedexperiment 1.24.0 r41hdfd78af_0 bioconda
bioconductor-xvector 0.34.0 r41h3be46a4_2 bioconda
bioconductor-zlibbioc 1.40.0 r41h3be46a4_2 bioconda
bwidget 1.9.14 h694c41f_1 conda-forge
bzip2 1.0.8 h0d85af4_4 conda-forge
c-ares 1.19.1 h0dc2134_0 conda-forge
ca-certificates 2023.7.22 h8857fd0_0 conda-forge
cairo 1.16.0 h09dd18c_1016 conda-forge
cctools_osx-64 973.0.1 ha1c5b94_14 conda-forge
clang 16.0.6 hc177806_1 conda-forge
clang-16 16.0.6 default_h762fdd7_1 conda-forge
clang_osx-64 16.0.6 h8787910_1 conda-forge
clangxx 16.0.6 default_h762fdd7_1 conda-forge
clangxx_osx-64 16.0.6 h1b7723c_1 conda-forge
compiler-rt 16.0.6 he1888fc_0 conda-forge
compiler-rt_osx-64 16.0.6 he1888fc_0 conda-forge
curl 8.2.1 h5f667d7_0 conda-forge
expat 2.5.0 hf0c8a7f_1 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 hab24e00_0 conda-forge
fontconfig 2.14.2 h5bb23bf_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
freetype 2.12.1 h3f81eb7_1 conda-forge
fribidi 1.0.10 hbcb3906_0 conda-forge
gettext 0.21.1 h8a4c099_0 conda-forge
gfortran_impl_osx-64 12.3.0 h54fd467_1 conda-forge
gfortran_osx-64 12.3.0 h18f7dce_1 conda-forge
gmp 6.2.1 h2e338ed_0 conda-forge
graphite2 1.3.13 h2e338ed_1001 conda-forge
gsl 2.7 h93259b0_0 conda-forge
harfbuzz 7.3.0 h413ba03_0 conda-forge
htslib 1.17 h365c357_2 bioconda
icu 72.1 h7336db1_0 conda-forge
isl 0.25 hb486fe8_0 conda-forge
krb5 1.21.2 hb884880_0 conda-forge
ld64_osx-64 609 ha20a434_14 conda-forge
lerc 4.0.0 hb486fe8_0 conda-forge
libblas 3.9.0 17_osx64_openblas conda-forge
libcblas 3.9.0 17_osx64_openblas conda-forge
libclang-cpp16 16.0.6 default_h762fdd7_1 conda-forge
libcurl 8.2.1 h5f667d7_0 conda-forge
libcxx 16.0.6 hd57cbcb_0 conda-forge
libdeflate 1.18 hac1461d_0 conda-forge
libedit 3.1.20191231 h0678c8f_2 conda-forge
libev 4.33 haf1e3a3_1 conda-forge
libexpat 2.5.0 hf0c8a7f_1 conda-forge
libffi 3.4.2 h0d85af4_5 conda-forge
libgfortran 5.0.0 12_3_0_h97931a8_1 conda-forge
libgfortran-devel_osx-64 12.3.0 h0b6f5ec_1 conda-forge
libgfortran5 12.3.0 hbd3c1fe_1 conda-forge
libglib 2.76.4 hc62aa5d_0 conda-forge
libiconv 1.17 hac89ed1_0 conda-forge
libjpeg-turbo 2.1.5.1 hb7f2c08_0 conda-forge
liblapack 3.9.0 17_osx64_openblas conda-forge
libllvm16 16.0.6 he4b1e75_2 conda-forge
libnghttp2 1.52.0 he2ab024_0 conda-forge
libopenblas 0.3.23 openmp_h429af6e_0 conda-forge
libpng 1.6.39 ha978bb4_0 conda-forge
libssh2 1.11.0 hd019ec5_0 conda-forge
libtiff 4.5.1 hf955e92_0 conda-forge
libwebp-base 1.3.1 h0dc2134_0 conda-forge
libxml2 2.11.5 hd95e348_0 conda-forge
libzlib 1.2.13 h8a1eda9_5 conda-forge
llvm-openmp 16.0.6 hff08bdf_0 conda-forge
llvm-tools 16.0.6 he4b1e75_2 conda-forge
make 4.3 h22f3db7_1 conda-forge
mpc 1.3.1 h81bd1dd_0 conda-forge
mpfr 4.2.0 h4f9bd69_0 conda-forge
ncurses 6.4 hf0c8a7f_0 conda-forge
openssl 3.1.2 h8a1eda9_0 conda-forge
pango 1.50.14 hbce5e75_1 conda-forge
pcre2 10.40 h1c4e4bc_0 conda-forge
pixman 0.40.0 hbcb3906_0 conda-forge
r-ashr 2.2_54 r41h49197e3_1 conda-forge
r-askpass 1.1 r41h815d134_3 conda-forge
r-base 4.1.3 had2b78c_10 conda-forge
r-bbmle 1.0.25 r41hc72bb7e_1 conda-forge
r-bdsmatrix 1.3_6 r41h815d134_1 conda-forge
r-bh 1.81.0_1 r41hc72bb7e_0 conda-forge
r-biocmanager 1.30.21 r41hc72bb7e_0 conda-forge
r-bit 4.0.5 r41h815d134_0 conda-forge
r-bit64 4.0.5 r41h815d134_1 conda-forge
r-bitops 1.0_7 r41h815d134_1 conda-forge
r-blob 1.2.4 r41hc72bb7e_0 conda-forge
r-cachem 1.0.8 r41h6dc245f_0 conda-forge
r-cli 3.6.1 r41h49197e3_0 conda-forge
r-coda 0.19_4 r41hc72bb7e_1 conda-forge
r-colorspace 2.1_0 r41h815d134_0 conda-forge
r-cpp11 0.4.3 r41hc72bb7e_0 conda-forge
r-crayon 1.5.2 r41hc72bb7e_1 conda-forge
r-curl 4.3.3 r41h0100ac3_2 conda-forge
r-dbi 1.1.3 r41hc72bb7e_1 conda-forge
r-dplyr 1.1.2 r41hac7d2d5_0 conda-forge
r-ellipsis 0.3.2 r41h815d134_1 conda-forge
r-emdbook 1.3.12 r41hc72bb7e_2 conda-forge
r-etrunct 0.1 r41hc72bb7e_1004 conda-forge
r-fansi 1.0.4 r41h815d134_0 conda-forge
r-farver 2.1.1 r41h49197e3_1 conda-forge
r-fastmap 1.1.1 r41h49197e3_0 conda-forge
r-formatr 1.14 r41hc72bb7e_0 conda-forge
r-futile.logger 1.4.3 r41hc72bb7e_1004 conda-forge
r-futile.options 1.0.1 r41hc72bb7e_1003 conda-forge
r-generics 0.1.3 r41hc72bb7e_1 conda-forge
r-ggplot2 3.4.2 r41hc72bb7e_0 conda-forge
r-ggridges 0.5.4 r41hc72bb7e_1 conda-forge
r-glue 1.6.2 r41h815d134_1 conda-forge
r-gtable 0.3.3 r41hc72bb7e_0 conda-forge
r-httr 1.4.6 r41hc72bb7e_0 conda-forge
r-invgamma 1.1 r41hc72bb7e_2 conda-forge
r-irlba 2.3.5.1 r41hce01bf1_0 conda-forge
r-isoband 0.2.7 r41h49197e3_1 conda-forge
r-jsonlite 1.8.5 r41h6dc245f_0 conda-forge
r-labeling 0.4.2 r41hc72bb7e_2 conda-forge
r-lambda.r 1.2.4 r41hc72bb7e_2 conda-forge
r-lattice 0.21_8 r41h815d134_0 conda-forge
r-lifecycle 1.0.3 r41hc72bb7e_1 conda-forge
r-locfit 1.5_9.7 r41h815d134_0 conda-forge
r-magrittr 2.0.3 r41h815d134_1 conda-forge
r-mass 7.3_58.3 r41h815d134_0 conda-forge
r-matrix 1.5_4.1 r41hc46c21c_0 conda-forge
r-matrixstats 1.0.0 r41h6dc245f_0 conda-forge
r-memoise 2.0.1 r41hc72bb7e_1 conda-forge
r-mgcv 1.8_42 r41h40f944a_0 conda-forge
r-mime 0.12 r41h815d134_1 conda-forge
r-mixsqp 0.3_48 r41hf5e6a41_0 conda-forge
r-munsell 0.5.0 r41hc72bb7e_1005 conda-forge
r-mvtnorm 1.2_2 r41hfe07776_0 conda-forge
r-nlme 3.1_162 r41h1e4e481_0 conda-forge
r-numderiv 2016.8_1.1 r41hc72bb7e_4 conda-forge
r-openssl 2.0.6 r41hfeb9312_0 conda-forge
r-pillar 1.9.0 r41hc72bb7e_0 conda-forge
r-pkgconfig 2.0.3 r41hc72bb7e_2 conda-forge
r-plogr 0.2.0 r41hc72bb7e_1004 conda-forge
r-plyr 1.8.8 r41h49197e3_0 conda-forge
r-png 0.1_8 r41hbf2103b_0 conda-forge
r-r6 2.5.1 r41hc72bb7e_1 conda-forge
r-rcolorbrewer 1.1_3 r41h785f33e_1 conda-forge
r-rcpp 1.0.10 r41h49197e3_0 conda-forge
r-rcpparmadillo 0.12.4.0.0 r41he9b8800_0 conda-forge
r-rcppeigen 0.3.3.9.3 r41h4f1a15b_0 conda-forge
r-rcppnumerical 0.5_0 r41h49197e3_0 conda-forge
r-rcurl 1.98_1.12 r41h0100ac3_1 conda-forge
r-restfulr 0.0.15 r41h5aaf88b_0 bioconda
r-rjson 0.2.21 r41h49197e3_2 conda-forge
r-rlang 1.1.1 r41hac7d2d5_0 conda-forge
r-rsqlite 2.3.1 r41h49197e3_0 conda-forge
r-scales 1.2.1 r41hc72bb7e_1 conda-forge
r-snow 0.4_4 r41hc72bb7e_1 conda-forge
r-squarem 2021.1 r41hc72bb7e_1 conda-forge
r-survival 3.5_5 r41h815d134_0 conda-forge
r-sys 3.4.2 r41h6dc245f_0 conda-forge
r-tibble 3.2.1 r41h815d134_1 conda-forge
r-tidyselect 1.2.0 r41hbe3e9c8_0 conda-forge
r-truncnorm 1.0_9 r41h815d134_0 conda-forge
r-utf8 1.2.3 r41h815d134_0 conda-forge
r-vctrs 0.6.2 r41hac7d2d5_0 conda-forge
r-viridislite 0.4.1 r41hc72bb7e_1 conda-forge
r-withr 2.5.0 r41hc72bb7e_1 conda-forge
r-xml 3.99_0.14 r41hb8526f4_1 conda-forge
r-xtable 1.8_4 r41hc72bb7e_4 conda-forge
r-yaml 2.3.7 r41h815d134_0 conda-forge
readline 8.2 h9e318b2_1 conda-forge
samtools 1.17 h25dfcfb_1 bioconda
sigtool 0.1.3 h88f4db0_0 conda-forge
tapi 1100.0.11 h9ce4665_0 conda-forge
tk 8.6.12 h5dbffcc_0 conda-forge
tktable 2.10 h49f0cf7_3 conda-forge
xz 5.2.6 h775f41a_0 conda-forge
zlib 1.2.13 h8a1eda9_5 conda-forge
zstd 1.5.2 h829000d_7 conda-forgeSo it looks like those packages are listed in the conda environment. I am quite new in dealing with command line installations, so there might be something I did wrong. Thanks for the support!
KevinXu264
commented
1 year ago @a-bio90
Are you building NanoBlot using Rstudio? If so, your conda environment is installed correctly, and you have set the R path to correctly include the conda environment path. I think this might have been an error on our end when we were building the Rstudio package dependencies, I don't think Rstudio correctly loads the packages in from the conda environment when pathed this way. Regardless, while we're figuring out this fix, can you try running this in the meantime in your Rstudio console?
BiocManager::install(c("BiocGenerics", "Rsamtools", "DESeq2", "GenomicAlignments", "GenomicRanges", "Rsubread"))
This should install all the missing dependencies in your Rstudio. Make sure you're still following the steps for the other packages (not native to Rstudio such as samtools, bedtools, etc.) Let us know if this works, and we'll follow-up with a more permanent solution to the original problem.
a-bio90
commented
1 year ago Yes, I am using Rstudio. I installed the packages with the command you suggested.
Then by running again devtools::install(build_vignettes = TRUE) to build NanoBlot I get the following error, where it says that the package rtracklayer is missing.
> devtools::install(build_vignettes = TRUE)
Skipping 6 packages not available: Rsubread, GenomicRanges, GenomicAlignments, DESeq2, Rsamtools, BiocGenerics
── R CMD build ──────────────────────────────────────────────────────────
✔ checking for file ‘/Users/bernarda/NanoBlot-main/NanoBlotPackage/DESCRIPTION’ (435ms)
─ preparing ‘NanoBlotPackage’:
✔ checking DESCRIPTION meta-information ...
─ installing the package to build vignettes
E creating vignettes (9.3s)
--- re-building ‘NanoBlotPackage.Rmd’ using rmarkdown
Program: samtools (Tools for alignments in the SAM format)
Version: 1.17 (using htslib 1.17)
Usage: samtools <command> [options]
Commands:
-- Indexing
dict create a sequence dictionary file
faidx index/extract FASTA
fqidx index/extract FASTQ
index index alignment
-- Editing
calmd recalculate MD/NM tags and '=' bases
fixmate fix mate information
reheader replace BAM header
targetcut cut fosmid regions (for fosmid pool only)
addreplacerg adds or replaces RG tags
markdup mark duplicates
ampliconclip clip oligos from the end of reads
-- File operations
collate shuffle and group alignments by name
cat concatenate BAMs
consensus produce a consensus Pileup/FASTA/FASTQ
merge merge sorted alignments
mpileup multi-way pileup
sort sort alignment file
split splits a file by read group
quickcheck quickly check if SAM/BAM/CRAM file appears intact
fastq converts a BAM to a FASTQ
fasta converts a BAM to a FASTA
import Converts FASTA or FASTQ files to SAM/BAM/CRAM
reference Generates a reference from aligned data
reset Reverts aligner changes in reads
-- Statistics
bedcov read depth per BED region
coverage alignment depth and percent coverage
depth compute the depth
flagstat simple stats
idxstats BAM index stats
cram-size list CRAM Content-ID and Data-Series sizes
phase phase heterozygotes
stats generate stats (former bamcheck)
ampliconstats generate amplicon specific stats
-- Viewing
flags explain BAM flags
head header viewer
tview text alignment viewer
view SAM<->BAM<->CRAM conversion
depad convert padded BAM to unpadded BAM
samples list the samples in a set of SAM/BAM/CRAM files
-- Misc
help [cmd] display this help message or help for [cmd]
version detailed version information
Quitting from lines 52-58 [unnamed-chunk-4] (NanoBlotPackage.Rmd)
Error: processing vignette 'NanoBlotPackage.Rmd' failed with diagnostics:
there is no package called 'rtracklayer'
--- failed re-building ‘NanoBlotPackage.Rmd’
SUMMARY: processing the following file failed:
‘NanoBlotPackage.Rmd’
Error: Vignette re-building failed.
Execution halted
Error in `(function (command = NULL, args = character(), error_on_status = TRUE, …`:
! System command 'R' failed
---
Exit status: 1
stdout & stderr: <printed>
---So I installed rtracklayer using BiocManager::install("rtracklayer"). Then running devtools::install(build_vignettes = TRUE) works with no errors, saying DONE (NanoBlotPackage). Now I can try to use you examples.
But just to be sure, when I open a new R project (in a different folder than the NanoBlot package) it will suffice to simply run library(NanoBlotPackage) to activate it or should I make other steps before?
I am very thankful for your suggestions and time I and hope to manage to use your cool tool in my research soon.
KevinXu264
commented
1 year ago That's great to hear. I forgot to mention the rtracklayer dependency as its used for one of the other tests. Running library(NanoBlotPackage) will suffice, there is no need to reinstall the package unless there is an update to the source code.
a-bio90
commented
1 year ago Thank, the examples ran smoothly now. In case I have unsolved issued with my analysis I might come back for a technical suggestion. Thanks a again for this resource.
Hello,
when trying to install NanoBlot in R after following the instructions I get the following error after running
[devtools](devtools::install(build_vignettes = TRUE)):Those packages are listed in
conda listin the nanoblot conda environment. Runningsystem2("samtools")works. It is probably something very stupid, any suggestion? Thanks