Introduction

This report checks if the status of packages on CRAN are due to intermittent failures.

Failures defined as warnings, notes or errors without change on:

  • R version used (if not stable the same svn snapshot)

  • The package version (Note that CRAN might modify a package without changing the version)

  • Their dependencies

Reasons of these failures might be because the packages depend on:

  • Random generation numbers

  • Flacky external resources

  • Other ?

Why is this important?

Because package maintainers of dependencies of that package, R core and CRAN team need to check if the failures are false positives.

This report started because it was suggested as something that the R-repositories working group could help the CRAN team.

Retrieve data

It makes use of tools::CRAN_check_results to retrieve the data.

library("dplyr")
library("tools", include.only = c("package_dependencies", "CRAN_check_results"))
library("flextable", include.only = c("flextable", "autofit"))
# Use a LOCAL environment to check if files can be overwritten on my computer
local_build <- as.logical(Sys.getenv("LOCAL", "FALSE"))
yc <- readRDS("today.RDS")
tc <- CRAN_check_results()
# Added 2023/03/09: sometimes some flavors are reported without status: Omit those
tc <- tc[!is.na(tc$Status),]
if (!interactive() && !local_build) {
  message("Saving today's file.")
  saveRDS(tc, file = "today.RDS")
}

The checks are from multiple flavors release, devel, old release and patched on multiple machines and configurations.

old_flavors <- readRDS("flavors.RDS")
flavors <- unique(tc$Flavor)
# One flavor now present in all is the r-devel-windows-x86_64: skip
flavors <- setdiff(flavors, "r-devel-windows-x86_64")
proto <- data.frame(r_version = character(),
                    os = character(),
                    architecture = character(),
                    other = character())
flavors_df <- strcapture(
  pattern = "r-([[:alnum:]]+)-([[:alnum:]]+)-([[:alnum:]_\\+]+)-?(.*)", 
  x = flavors,
  proto = proto)

# Extract R version used and svn id
h <- "https://www.r-project.org/nosvn/R.check/%s/ggplot2-00check.html"
links <- sprintf(h, flavors)
extract_revision <- function(x) {
  r <- readLines(x, 12)[12]
  version <- strcapture(pattern = "([[:digit:]]\\.[[:digit:]]\\.[[:digit:]])",  
                        x = r, proto = data.frame(version = character()))
  revision <- strcapture(pattern = "(r[[:digit:]]+)",  x = r,
                         proto = data.frame(revision = character()))
  cbind(version, revision)
}
revision <- data.frame(version = character(),
                       revision = character())
for (i in links) {
  revision <- rbind(revision, extract_revision(i))
}

flavors_df <- cbind(flavors = flavors, flavors_df, revision)
if (!interactive() && !local_build) {
  saveRDS(flavors_df, "flavors.RDS")
}

m <- match(tc$Flavor, flavors_df$flavors)
tc_flavors <- cbind(tc, flavors_df[m, ])
flextable(flavors_df) |> 
  autofit()

flavors

r_version

os

architecture

other

version

revision

r-devel-linux-x86_64-debian-clang

devel

linux

x86_64

debian-clang

r89703

r-devel-linux-x86_64-debian-gcc

devel

linux

x86_64

debian-gcc

r89703

r-devel-linux-x86_64-fedora-clang

devel

linux

x86_64

fedora-clang

r89680

r-devel-linux-x86_64-fedora-gcc

devel

linux

x86_64

fedora-gcc

r89685

r-devel-macos-arm64

devel

macos

arm64

r89366

r-patched-linux-x86_64

patched

linux

x86_64

4.5.3

r89696

r-release-linux-x86_64

release

linux

x86_64

4.5.3

r-release-macos-arm64

release

macos

arm64

4.5.2

r-release-macos-x86_64

release

macos

x86_64

4.5.1

r-release-windows-x86_64

release

windows

x86_64

4.5.3

r-oldrel-macos-arm64

oldrel

macos

arm64

4.4.3

r-oldrel-macos-x86_64

oldrel

macos

x86_64

4.4.1

r-oldrel-windows-x86_64

oldrel

windows

x86_64

4.4.3

r89426

It assumes that the same configuration in one package is used for all. Or in other words that the reports of the configuration (svn revision and version) for the A3 package is the same as for all the other packages.

Warning: This assumption is not always true, but this would require to check each log file on each flavor to verify the R and svn id of each package (which could take too much time and resources).

Overview

Briefly an introduction of how much effort goes into checking

library("ggplot2")
theme_set(theme_minimal())
tc |> 
  filter(!is.na(T_install)) |> 
  ggplot() +
  geom_violin(aes(T_install, Flavor)) +
  scale_x_log10() +
  labs(x = "seconds", title = "Time to install", y = element_blank())
Machines (y axis) vs install time (seconds, x axis), violing plot usually around 10 seconds.

Distribution of install time on each machine.

This means that just to install all the packages on the multiple flavors with a single CPU would take 67 days.

tc |> 
  filter(!is.na(T_check)) |> 
  ggplot() +
  geom_violin(aes(T_check, Flavor), trim = FALSE) +
  scale_x_log10() +
  labs(x = "seconds", title = "Time to check", y = element_blank())
Machines (y axis) vs check time (seconds, x axis), violing plot usually around 100 seconds.

Distribution of checking time on each machine.

This means that to check all the packages on the multiple flavors with a single CPU would take 353 days.

tc |> 
  filter(!is.na(T_total)) |> 
  ggplot() +
  geom_violin(aes(T_total, Flavor)) +
  scale_x_log10() +
  labs(x = "seconds", title = "Time to check and install", y = element_blank())
Machines (y axis) vs total time (seconds, x axis), violing plot usually around 100 seconds.

Distribution of total time on each machine.

This means that to install and check all the packages with a single CPU would take 433 days.

I don’t know the computational cost of 266 days of CPU (every day), but a rough calculation of 2.5 cents per hour means 259.57 dollars daily dedicated to this.

tc |> 
  group_by(Package) |> 
  summarize(Versions = n_distinct(Version)) |> 
  ungroup() |> 
  count(Versions, name = "Packages", sort = TRUE) |> 
  flextable() |> 
  autofit()

Versions

Packages

1

22,992

2

437

3

7

4

1

This was surprising, but sometimes checks have multiple versions. Probably when a new version is added and the system don’t catch it for a certain machine.

tc |> 
  group_by(Package) |> 
  summarize(Flavors = n_distinct(Flavor)) |> 
  ungroup() |> 
  count(Flavors, name = "Packages", sort = TRUE) |> 
  flextable() |> 
  autofit()

Flavors

Packages

14

23,249

11

56

12

53

13

22

8

20

3

12

4

8

10

8

9

6

5

2

6

1

Similarly, often packages are only tested on few configurations.

Combining both we can have packages with few configurations that have multiple versions being tested.

tc |> 
  group_by(Package) |> 
  summarize(Versions = as.character(n_distinct(Version)),
            Flavors = n_distinct(Flavor)) |> 
  ungroup() |> 
  count(Flavors, Versions, name = "Packages") |> 
  ggplot() +
  geom_tile(aes(Flavors, Versions, fill = log10(Packages))) +
  scale_x_continuous(expand = expansion())
Flavors of machines and versions of packages

Most packages are just tested one version.

But focusing on those that have just one version of the package being tested, most of the machines have packages either OK or with some notes.

man_colors <- c("OK" = "green", "NOTE" = "darkgreen", 
                "WARNING" = "yellow", "ERROR" = "red", "FAILURE" = "black")
tc |> 
  group_by(Package) |> 
  filter(n_distinct(Version) == 1) |> 
  ungroup() |> 
  group_by(Flavor) |> 
  count(Status, name = "packages") |> 
  mutate(perc = packages/sum(packages),
         Status = forcats::fct_relevel(Status, names(man_colors))) |> 
  ggplot() + 
  geom_col(aes(perc, Flavor, fill = Status)) +
  scale_x_continuous(expand = expansion(), labels = scales::percent_format()) +
  scale_fill_manual(values = man_colors) +
  labs(title = "Packages check status", x = element_blank())
On the vertical axis the machine, on the horitzonal axis the packages colored by the status.

Most frequent status is OK or NOTE on all machines.

If we look at the most frequent status report for packages we can see this table:

ts <- tc |> 
  group_by(Package) |> 
  filter(n_distinct(Version) == 1) |> 
  count(Status, name = "flavors") |> 
  ungroup() |> 
  tidyr::pivot_wider(values_from = flavors, names_from = Status, 
                     values_fill = 0) |> 
  count(OK, NOTE, WARNING, ERROR, FAILURE, name = "packages", sort = TRUE)
download.file("https://cran.r-project.org/web/packages/packages.rds", 
              destfile = "packages.RDS") # From the help page
ap <- readRDS("packages.RDS") |> 
  as.data.frame() |> 
  distinct(Package, .keep_all = TRUE)
ap_bioc <- available.packages(repos = BiocManager::repositories()[1:5])
ap_bioc <- cbind(ap_bioc, Additional_repositories = NA)
ap_colm <- intersect(colnames(ap), colnames(ap_bioc))
ap <- rbind(ap[, ap_colm], ap_bioc[, ap_colm])
head(ts) |> 
  flextable() |> 
  autofit()

OK

NOTE

WARNING

ERROR

FAILURE

packages

14

0

0

0

0

13,511

12

2

0

0

0

4,379

11

3

0

0

0

1,531

0

14

0

0

0

932

9

5

0

0

0

780

10

4

0

0

0

288

We can see that the most common occurrences are some sort of OK and notes on checks. We can also check the official results on CRAN.

We can see that 0.98%, 0.68%, 0.08%, 0.02%, 0.02% of packages pass all checks without notes.

Now let’s see which of the notes or failures are due to intermittent issues.

Compare

First we need to make sure that we compare the right configurations. They must be the same machine, the same R version and the same svn revision between yesterday and today.

# Compare the previous flavor with today's
m_flavor <- which(flavors_df$flavors %in% old_flavors$flavors)
m_version <- which(flavors_df$version %in% old_flavors$version)
m_revision <- which(flavors_df$revision %in% old_flavors$revision)
tm <- table(c(m_flavor, m_version, m_revision))
compare <- flavors_df$flavors[tm == 3] # Only missing the packages version

All changes

Next, compare the status of the packages if the version of the package is the same.

# Find package on the flavors to compare that haven't changed versions
library("dplyr")
tcc <- filter(tc, Flavor %in% compare) |> 
  select(Flavor, Package, Version, Status) |> 
  arrange(Flavor, Package)
ycc <- filter(yc, Flavor %in% compare) |> 
  select(Flavor, Package, Version, Status) |> 
  arrange(Flavor, Package)

all_checks <- merge(tcc, ycc, by = c("Flavor", "Package"), 
                    suffixes = c(".t", ".y"), all = TRUE) 

possible_packages <- all_checks |> 
  filter(Version.t == Version.y & # Same version
           Status.t != Status.y & # Different status
           !is.na(Status.y) & # No new version or removed package
           !is.na(Status.t)) |> 
  rename(Today = Status.t, Yesterday = Status.y)
possible_packages |> 
  select(Package, Flavor, Today, Yesterday, -Version.t, -Version.y) |> 
  arrange(Package, Flavor) |> 
  flextable() |> 
  autofit()

Package

Flavor

Today

Yesterday

AssumpSure

r-devel-linux-x86_64-fedora-clang

ERROR

NOTE

BFS

r-devel-linux-x86_64-debian-clang

OK

ERROR

BFpack

r-devel-linux-x86_64-fedora-clang

ERROR

OK

BIFIEsurvey

r-devel-linux-x86_64-fedora-clang

ERROR

OK

BIFIEsurvey

r-devel-linux-x86_64-fedora-gcc

NOTE

OK

BayLum

r-devel-linux-x86_64-fedora-clang

ERROR

OK

BayesRep

r-devel-linux-x86_64-fedora-clang

ERROR

OK

BayesRepDesign

r-devel-linux-x86_64-fedora-clang

ERROR

OK

BeeBDC

r-devel-linux-x86_64-debian-clang

ERROR

OK

BeeBDC

r-devel-linux-x86_64-fedora-clang

ERROR

OK

CDM

r-devel-linux-x86_64-fedora-clang

ERROR

OK

CTTShiny

r-devel-linux-x86_64-fedora-clang

ERROR

OK

CausalGPS

r-devel-linux-x86_64-fedora-clang

ERROR

OK

ClimMobTools

r-devel-linux-x86_64-debian-clang

OK

NOTE

CryptRndTest

r-devel-linux-x86_64-fedora-clang

ERROR

OK

DDIwR

r-devel-linux-x86_64-fedora-clang

ERROR

OK

DIFshiny

r-devel-linux-x86_64-fedora-clang

ERROR

OK

DandEFA

r-devel-linux-x86_64-fedora-clang

ERROR

OK

EFA.dimensions

r-devel-linux-x86_64-fedora-clang

ERROR

OK

EQUALPrognosis

r-devel-linux-x86_64-fedora-clang

ERROR

OK

FAfA

r-devel-linux-x86_64-fedora-clang

ERROR

OK

FactorCopula

r-devel-linux-x86_64-fedora-clang

ERROR

OK

GDILM.SEIRS

r-devel-linux-x86_64-debian-clang

ERROR

OK

GDINA

r-devel-linux-x86_64-fedora-clang

ERROR

OK

GPCMlasso

r-devel-linux-x86_64-fedora-clang

ERROR

OK

GRShiny

r-devel-linux-x86_64-fedora-clang

ERROR

OK

IMTest

r-devel-linux-x86_64-fedora-clang

ERROR

NOTE

IRTShiny

r-devel-linux-x86_64-fedora-clang

ERROR

OK

LAM

r-devel-linux-x86_64-fedora-clang

ERROR

OK

LambertW

r-devel-linux-x86_64-fedora-clang

ERROR

OK

LambertW

r-devel-linux-x86_64-fedora-gcc

NOTE

OK

LikertMakeR

r-devel-linux-x86_64-fedora-clang

ERROR

OK

LindleyPowerSeries

r-devel-linux-x86_64-fedora-clang

ERROR

OK

LongDat

r-devel-linux-x86_64-fedora-clang

ERROR

OK

Luminescence

r-devel-linux-x86_64-fedora-clang

ERROR

OK

MCCM

r-devel-linux-x86_64-fedora-clang

ERROR

OK

MiscMetabar

r-devel-linux-x86_64-fedora-clang

ERROR

OK

MultBiplotR

r-devel-linux-x86_64-fedora-clang

ERROR

OK

NFWdist

r-devel-linux-x86_64-fedora-clang

ERROR

OK

OSLdecomposition

r-devel-linux-x86_64-fedora-clang

ERROR

OK

PCMRS

r-devel-linux-x86_64-fedora-clang

ERROR

OK

PGaGEV

r-devel-linux-x86_64-fedora-clang

ERROR

OK

PLMIX

r-devel-linux-x86_64-debian-clang

OK

ERROR

PLmixed

r-devel-linux-x86_64-fedora-clang

ERROR

OK

PairViz

r-oldrel-macos-x86_64

OK

ERROR

PerFit

r-devel-linux-x86_64-fedora-clang

ERROR

OK

ProjectTemplate

r-devel-linux-x86_64-debian-clang

ERROR

NOTE

PytrendsLongitudinalR

r-devel-linux-x86_64-debian-clang

ERROR

OK

QuickJSR

r-devel-linux-x86_64-debian-clang

ERROR

OK

RLumShiny

r-devel-linux-x86_64-fedora-clang

ERROR

OK

RSP

r-devel-linux-x86_64-fedora-clang

ERROR

OK

RcppTskit

r-devel-linux-x86_64-debian-clang

ERROR

OK

RelDists

r-devel-linux-x86_64-fedora-clang

ERROR

OK

SIAmodules

r-devel-linux-x86_64-fedora-clang

ERROR

OK

SetMethods

r-devel-linux-x86_64-fedora-clang

ERROR

OK

Spower

r-devel-linux-x86_64-fedora-clang

ERROR

OK

TDCM

r-devel-linux-x86_64-fedora-clang

ERROR

OK

TSQCA

r-devel-linux-x86_64-fedora-clang

FAILURE

OK

TestAnaAPP

r-devel-linux-x86_64-fedora-clang

ERROR

OK

TransProR

r-devel-linux-x86_64-fedora-clang

ERROR

OK

UGarima

r-devel-linux-x86_64-fedora-clang

ERROR

OK

UPCM

r-devel-linux-x86_64-fedora-clang

ERROR

OK

WordOfMouth

r-devel-linux-x86_64-fedora-clang

ERROR

OK

a5R

r-release-macos-arm64

OK

ERROR

aebdata

r-devel-linux-x86_64-debian-clang

OK

ERROR

algaeClassify

r-devel-linux-x86_64-debian-clang

ERROR

OK

amVennDiagram5

r-devel-linux-x86_64-fedora-clang

ERROR

OK

annotaR

r-devel-linux-x86_64-debian-clang

ERROR

OK

arules

r-devel-linux-x86_64-debian-clang

OK

NOTE

arules

r-devel-linux-x86_64-fedora-clang

OK

NOTE

aspect

r-devel-linux-x86_64-fedora-clang

ERROR

OK

bellreg

r-devel-linux-x86_64-fedora-clang

ERROR

NOTE

bestNormalize

r-devel-linux-x86_64-fedora-clang

ERROR

OK

bfpwr

r-devel-linux-x86_64-fedora-clang

ERROR

OK

biogrowth

r-devel-linux-x86_64-fedora-clang

ERROR

OK

bundle

r-devel-linux-x86_64-debian-clang

ERROR

OK

cSEM

r-devel-linux-x86_64-fedora-clang

ERROR

NOTE

catIrt

r-devel-linux-x86_64-fedora-clang

ERROR

OK

catSurv

r-devel-linux-x86_64-fedora-clang

ERROR

OK

copernicusR

r-devel-linux-x86_64-debian-clang

ERROR

OK

difR

r-devel-linux-x86_64-fedora-clang

ERROR

OK

dina

r-devel-linux-x86_64-fedora-clang

ERROR

OK

dina

r-devel-linux-x86_64-fedora-gcc

NOTE

OK

discnorm

r-devel-linux-x86_64-fedora-clang

ERROR

OK

dsBase

r-devel-linux-x86_64-fedora-clang

ERROR

OK

dsTidyverse

r-devel-linux-x86_64-fedora-clang

ERROR

OK

dsTidyverseClient

r-devel-linux-x86_64-fedora-clang

ERROR

OK

duckplyr

r-devel-linux-x86_64-debian-clang

OK

ERROR

epmfd

r-devel-linux-x86_64-fedora-clang

ERROR

OK

equateIRT

r-devel-linux-x86_64-fedora-clang

ERROR

OK

equateMultiple

r-devel-linux-x86_64-fedora-clang

ERROR

OK

fastshap

r-devel-linux-x86_64-debian-clang

ERROR

OK

filibustr

r-devel-linux-x86_64-debian-clang

ERROR

OK

fioRa

r-devel-linux-x86_64-debian-clang

ERROR

OK

frair

r-devel-linux-x86_64-fedora-clang

ERROR

OK

genpathmox

r-devel-linux-x86_64-fedora-clang

ERROR

OK

ggVennDiagram

r-devel-linux-x86_64-fedora-clang

ERROR

OK

ggdag

r-devel-linux-x86_64-debian-clang

OK

ERROR

ggpicrust2

r-devel-linux-x86_64-fedora-clang

ERROR

OK

gosset

r-devel-linux-x86_64-debian-clang

OK

ERROR

immer

r-devel-linux-x86_64-fedora-clang

NOTE

OK

immer

r-devel-linux-x86_64-fedora-gcc

NOTE

OK

irtreliability

r-devel-linux-x86_64-fedora-clang

ERROR

OK

itemanalysis

r-devel-linux-x86_64-fedora-clang

ERROR

OK

iterors

r-devel-linux-x86_64-debian-clang

ERROR

OK

kequate

r-devel-linux-x86_64-fedora-clang

ERROR

OK

latdiag

r-devel-linux-x86_64-fedora-clang

ERROR

OK

lava

r-devel-linux-x86_64-fedora-clang

ERROR

OK

lefko3

r-devel-linux-x86_64-fedora-gcc

NOTE

OK

lsasim

r-devel-linux-x86_64-fedora-clang

ERROR

OK

manydata

r-devel-linux-x86_64-fedora-clang

ERROR

OK

mdmb

r-devel-linux-x86_64-fedora-clang

NOTE

OK

mdmb

r-devel-linux-x86_64-fedora-gcc

NOTE

OK

miniCRAN

r-devel-linux-x86_64-debian-clang

ERROR

OK

missCompare

r-devel-linux-x86_64-fedora-clang

ERROR

OK

mixtree

r-devel-linux-x86_64-fedora-clang

FAILURE

OK

mtrank

r-devel-linux-x86_64-debian-clang

OK

ERROR

neuralGAM

r-devel-linux-x86_64-debian-clang

ERROR

OK

optband

r-devel-linux-x86_64-fedora-clang

ERROR

OK

otargen

r-devel-linux-x86_64-debian-clang

ERROR

OK

pairwiseLLM

r-devel-linux-x86_64-fedora-clang

ERROR

OK

pangoling

r-devel-linux-x86_64-debian-clang

ERROR

OK

peermodels

r-devel-linux-x86_64-fedora-clang

ERROR

OK

peermodels

r-devel-linux-x86_64-fedora-gcc

ERROR

OK

phytoclass

r-devel-linux-x86_64-fedora-clang

ERROR

OK

pmml

r-devel-macos-arm64

OK

ERROR

polycor

r-devel-linux-x86_64-fedora-clang

ERROR

OK

rbrsa

r-devel-linux-x86_64-debian-clang

ERROR

OK

rbrsa

r-devel-linux-x86_64-fedora-clang

FAILURE

OK

rfriend

r-devel-linux-x86_64-fedora-clang

WARNING

OK

rfriend

r-devel-linux-x86_64-fedora-gcc

WARNING

OK

rpanel

r-devel-linux-x86_64-fedora-clang

ERROR

OK

rpanel

r-devel-linux-x86_64-fedora-gcc

ERROR

OK

rsurv

r-devel-linux-x86_64-fedora-clang

ERROR

NOTE

sandbox

r-devel-linux-x86_64-fedora-clang

FAILURE

OK

sem

r-devel-linux-x86_64-fedora-clang

ERROR

OK

sfsmisc

r-devel-linux-x86_64-fedora-clang

ERROR

OK

sgr

r-devel-linux-x86_64-fedora-clang

ERROR

OK

shinyIRT

r-devel-linux-x86_64-fedora-clang

ERROR

OK

shortIRT

r-devel-linux-x86_64-fedora-clang

ERROR

OK

shorts

r-devel-linux-x86_64-fedora-clang

ERROR

OK

simDAG

r-devel-linux-x86_64-fedora-clang

ERROR

OK

singleRcapture

r-devel-linux-x86_64-fedora-clang

ERROR

OK

sirt

r-devel-linux-x86_64-fedora-clang

ERROR

OK

sirt

r-devel-linux-x86_64-fedora-gcc

NOTE

OK

subscore

r-devel-linux-x86_64-fedora-clang

ERROR

OK

tidySEM

r-devel-linux-x86_64-fedora-clang

ERROR

OK

tidynorm

r-devel-linux-x86_64-debian-clang

ERROR

OK

tinytest2JUnit

r-devel-linux-x86_64-debian-clang

ERROR

OK

tm.plugin.mail

r-devel-linux-x86_64-debian-clang

ERROR

OK

treespace

r-devel-linux-x86_64-fedora-clang

ERROR

OK

tsbox

r-devel-linux-x86_64-debian-clang

NOTE

OK

umx

r-devel-linux-x86_64-fedora-clang

ERROR

NOTE

venn

r-devel-linux-x86_64-fedora-clang

ERROR

OK

xhaz

r-devel-linux-x86_64-fedora-clang

ERROR

OK

xplainfi

r-devel-linux-x86_64-debian-clang

NOTE

OK

If the machine and R versions is the same but the check of the package is different there might be some discrepancy between the dependencies.

# Extract dependencies
dependencies <- package_dependencies(unique(possible_packages$Package),
                                     # Should it check all the recursive dependencies or only direct?
                                     db = ap, # Only considering those dependencies on CRAN and Bioconductor but not any Additional_repositories. 
                                     recursive = TRUE, 
                                     which = c("Depends", "Imports", "LinkingTo", "Suggests"))

# Prepare to compare versions (as they are sorted by everything else we can compare directly)
intermittent_failures <- rep(FALSE, length(dependencies))
names(intermittent_failures) <- names(dependencies)
dep_0 <- lengths(dependencies) == 0
intermittent_failures[dep_0] <- TRUE

If they do not have any recursive dependency on Depends, Imports, LinkingTo and Suggests they might be have some intermittent problems on the packages. These is only on dependencies on CRAN and Bioconductor but not in other additional repositories (There are 191 packages with additional repositories).

If they have some dependencies and those dependencies didn’t change as far as we can tell then there might be some problems with random numbers or connectivity.

for (pkg in names(intermittent_failures[!intermittent_failures])) {
  dep <- dependencies[[pkg]]
  fl <- possible_packages$Flavor[possible_packages$Package == pkg]
  intermittent_failures[pkg] <- all_checks |> 
    filter(Package %in% dep,
           Flavor %in% fl,
           Version.t == Version.y,
           Status.t != Status.y) |> 
    nrow() == 0 # If packages outside || any(!dep %in% rownames(ap)) 
}
packages <- names(intermittent_failures)[intermittent_failures]

We finally show the differences on the status of those without any dependency change on version or status1:

keep_files <- filter(possible_packages, Package %in% packages) |> 
  merge(y = flavors_df, by.x = "Flavor", by.y = "flavors", all.x = TRUE, all.y = FALSE) |> 
  select(Package, Flavor, Version = Version.t, R_version = r_version, OS = os, 
         architecture, other, version, revision) |> 
  mutate(Date = Sys.time())

if (nrow(keep_files >= 1)) {
  write.csv(keep_files, 
            paste0("cran-failing-", format(Sys.time(), "%Y%m%dT%H%M"), ".csv"),
            row.names = FALSE,
            quote = FALSE,
  )
}
filter(possible_packages, Package %in% packages) |> 
  select(Package, Flavor, Today, Yesterday, -Version.t, -Version.y) |> 
  flextable() |> 
  autofit()

Package

Flavor

Today

Yesterday

tinytest2JUnit

r-devel-linux-x86_64-debian-clang

ERROR

OK

PairViz

r-oldrel-macos-x86_64

OK

ERROR

a5R

r-release-macos-arm64

OK

ERROR

Conclusion

cat("There are no packages detected with differences between yesterday and today attributable to intermittent failures.\n")
knitr::knit_exit()
cat("This suggests that these packages might have some problems with random numbers or connectivity:\n\n")

This suggests that these packages might have some problems with random numbers or connectivity:

if (any(dep_0)) {
  cat("\n## Packages with dependencies\n\n")
  cat(paste0(" - ", sort(intersect(packages, 
                                   names(dependencies)[dep_0])), "\n"), sep = "")
  cat("\n## Packages without dependencies\n\n")
  cat(paste0(" - ", sort(intersect(packages,
                                   names(dependencies)[!dep_0])), "\n"), sep = "")
  
} else {
  cat(paste0(" - ", sort(packages), "\n"), sep = "")
}
  • a5R
  • PairViz
  • tinytest2JUnit

  1. I think a new version might not propagate to check other packages until 24 hours later as checks might have already started for that day.↩︎