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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2156/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TSAR 1.3.0  (landing page)
Xinlin Gao
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/TSAR
git_branch: devel
git_last_commit: dfc1f3d
git_last_commit_date: 2024-04-30 11:51:46 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for TSAR on palomino4

To the developers/maintainers of the TSAR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TSAR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: TSAR
Version: 1.3.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TSAR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings TSAR_1.3.0.tar.gz
StartedAt: 2024-06-10 11:41:43 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 11:49:50 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 486.9 seconds
RetCode: 0
Status:   OK  
CheckDir: TSAR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TSAR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings TSAR_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/TSAR.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'TSAR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TSAR' version '1.3.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'TSAR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Found the following CITATION file in a non-standard place:
  CITATION
Most likely 'inst/CITATION' should be used instead.
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
TSA_Tms : <anonymous>: no visible binding for global variable 'well_ID'
TSA_Tms : <anonymous>: no visible binding for global variable 'Tm'
TSA_Tms : <anonymous>: no visible global function definition for 'sd'
TSA_Tms: no visible binding for global variable 'well_ID'
TSA_Tms: no visible binding for global variable 'Tm'
TSA_Tms: no visible binding for global variable 'condition_ID'
TSA_Tms: no visible binding for global variable 'Protein'
TSA_Tms: no visible binding for global variable 'Ligand'
TSA_average: no visible binding for global variable 'Temperature'
TSA_average: no visible binding for global variable 'Fluorescence'
TSA_average: no visible global function definition for 'sd'
TSA_average: no visible binding for global variable 'Normalized'
TSA_average: no visible global function definition for 'predict'
TSA_boxplot: no visible binding for global variable 'condition_ID'
TSA_boxplot: no visible binding for global variable 'Tm'
TSA_boxplot: no visible binding for global variable 'Ligand'
TSA_boxplot: no visible binding for global variable 'well_ID'
TSA_boxplot: no visible binding for global variable 'Protein'
TSA_compare_plot: no visible binding for global variable 'Temperature'
TSA_compare_plot: no visible binding for global variable 'avg_smooth'
TSA_compare_plot: no visible binding for global variable
  'sd_min_smooth'
TSA_compare_plot: no visible binding for global variable
  'sd_max_smooth'
TSA_compare_plot: no visible global function definition for
  'colorRampPalette'
TSA_wells_plot: no visible binding for global variable 'Temperature'
TSA_wells_plot: no visible binding for global variable 'Fluorescence'
TSA_wells_plot: no visible binding for global variable 'Normalized'
TSA_wells_plot: no visible binding for global variable 'well_ID'
TSA_wells_plot: no visible binding for global variable 'sd_min_smooth'
TSA_wells_plot: no visible binding for global variable 'sd_max_smooth'
TSA_wells_plot: no visible binding for global variable 'avg_smooth'
TSA_wells_plot: no visible binding for global variable 'sd_min'
TSA_wells_plot: no visible binding for global variable 'sd_max'
TSA_wells_plot: no visible binding for global variable 'average'
build_curves: no visible binding for global variable 'condition_ID'
build_table: no visible global function definition for 'head'
build_well: no visible global function definition for 'head'
dummy_plot: no visible binding for global variable 'x'
dummy_plot: no visible binding for global variable 'y'
gam_analysis : process_well: no visible binding for global variable
  'Well.Position'
gam_analysis : process_well: no visible global function definition for
  'all_of'
join_well_info: no visible binding for global variable 'Col'
join_well_info: no visible binding for global variable 'pos'
join_well_info: no visible binding for global variable 'Well'
join_well_info: no visible binding for global variable 'Protein'
join_well_info: no visible binding for global variable 'Ligand'
join_well_info: no visible global function definition for 'na.omit'
merge_norm : <anonymous>: no visible global function definition for
  'read.csv'
merge_norm : <anonymous>: no visible binding for global variable
  'Well.Position'
merge_norm : <anonymous>: no visible binding for global variable
  'Protein'
merge_norm : <anonymous>: no visible binding for global variable
  'Ligand'
merge_norm: no visible binding for global variable 'tm'
merge_norm: no visible binding for global variable 'Well.Position'
merge_update: no visible global function definition for 'na.omit'
model_boltzmann: no visible binding for global variable 'Temperature'
normalize: no visible global function definition for 'all_of'
preview_condition: no visible global function definition for 'head'
preview_model: no visible binding for global variable 'Well.Position'
read_analysis: no visible global function definition for 'read.delim'
read_analysis: no visible global function definition for 'read.csv'
read_raw_data: no visible global function definition for 'read.delim'
read_raw_data: no visible global function definition for 'read.csv'
remove_raw: no visible binding for global variable 'Well.Position'
remove_raw: no visible binding for global variable 'Well'
remove_selected_graph: no visible binding for global variable
  'condition_ID'
remove_selected_graph: no visible binding for global variable 'well_ID'
screen: no visible binding for global variable 'Well.Position'
screen: no visible binding for global variable 'Well'
screen : normalize_by_well: no visible binding for global variable
  'Well.Position'
screen: no visible binding for global variable 'Temperature'
screen: no visible binding for global variable 'Fluorescence'
view_deriv: no visible binding for global variable 'Temperature'
view_deriv: no visible binding for global variable 'norm_deriv'
view_deriv: no visible binding for global variable 'well_ID'
view_deriv: no visible binding for global variable 'Tm'
view_model: no visible binding for global variable 'Temperature'
view_model: no visible binding for global variable 'Normalized'
view_model: no visible binding for global variable 'fitted'
view_model: no visible global function definition for 'na.omit'
view_model: no visible binding for global variable 'norm_deriv'
view_model: no visible binding for global variable 'Well.Position'
Undefined global functions or variables:
  Col Fluorescence Ligand Normalized Protein Temperature Tm Well
  Well.Position all_of average avg_smooth colorRampPalette condition_ID
  fitted head na.omit norm_deriv pos predict read.csv read.delim sd
  sd_max sd_max_smooth sd_min sd_min_smooth tm well_ID x y
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "fitted", "na.omit", "predict", "sd")
  importFrom("utils", "head", "read.csv", "read.delim")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
TSA_wells_plot 22.84   1.35   24.18
gam_analysis   10.21   0.53   10.73
view_deriv      5.68   1.39    8.64
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/TSAR.Rcheck/00check.log'
for details.


Installation output

TSAR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL TSAR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'TSAR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (TSAR)

Tests output

TSAR.Rcheck/tests/testthat.Rout


R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(TSAR)

Attaching package: 'TSAR'

The following object is masked from 'package:graphics':

    screen

> 
> test_check("TSAR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ]
> 
> proc.time()
   user  system elapsed 
  12.32   17.45   29.76 

Example timings

TSAR.Rcheck/TSAR-Ex.timings

nameusersystemelapsed
TSA_Tms0.391.001.39
TSA_boxplot1.191.162.34
TSA_ligands0.331.031.36
TSA_proteins0.270.921.19
TSA_wells_plot22.84 1.3524.18
Tm_difference0.300.981.28
Tm_est1.340.051.40
analyze_norm000
condition_IDs0.451.051.50
gam_analysis10.21 0.5310.73
get_legend0.720.821.56
graph_tsar000
join_well_info1.070.321.39
merge_norm1.140.001.14
merge_tsa000
model_boltzmann0.080.000.08
model_fit1.360.041.41
model_gam1.530.041.56
normalize0.100.000.09
normalize_fluorescence000
read_analysis000
read_raw_data000
read_tsar0.480.010.50
remove_raw0.590.240.83
rescale000
run_boltzmann0.10.00.1
screen1.050.011.06
tsa_average0.751.161.91
tsa_compare_plot2.811.093.91
view_deriv5.681.398.64
view_model1.780.081.86
weed_raw0.040.000.04
well_IDs0.381.121.55
write_tsar0.720.020.73